The Coordinate Manipulation Commands The commands in this section are primarily used for moving some or all of the atoms. There is a wide range of commands and options. All of the commands may be used on either the main coordinate set, or the comparison set. Some commands require both sets of coordinates. * Syntax / Syntax of the coordinate manipulations commands * Simple / Descriptions of the simple commands * Function / Descriptions of the remaining commands * Substitutions / Description and usage of substitution values
Top Syntax of Coordinate Manipulation commands [SYNTAX COORdinate manipulation] COORdinates { INITialize } [COMP] [DIMS] [atom-selection] { COPY } [WEIGhting_array] { SWAP } [IMAGes] [SECOnd] { AVERage [ FACT real ] } { SCALe [ FACT real ] } { MASS_weighting } { ADD } { SET vector-spec } { TRANslate vector-spec } { ROTAte vector-spec {PHI real} } { {MATRix} } { TWISt vector-spec RATE real } { ORIEnt [MASS] [RMS] [NOROtation] } { RMS [MASS] } { TMSCore } { UFSR } { DIFFerence } { FORCe [MASS] } { SHAKe [MASS] } { DRAW draw-spec } { DISTance distance-spec [DIFF] } { DIPOle [OXYZ] [MASS] } { MINDist distance-spec } { MAXDist distance-spec } { READ io-specification } { WRITe io-specification } { PRINt io-specification } { RGYR [MASS] [FACT <real>] } { OPERate image_name } { STATistics [MASS] } { VOLUme {SPACe integer} } { } { DUPLicate { 2X(atom-selection) } } { { PREVious } } { DISTance RESIdue CUT <real> [2X](atom-selection) } { DRMS [2X](atom-selection) } COORdinates HISTogram { X } [IUNIt int] HMIN real HMAX real HNUM integer - { Y } [HSAVe] [HPRInt] [HNORm real] [HDENsity real] - { Z } [COMP] [WEIGhting_array] atom_selection { R } COORdinates { HBONd } [CUTHB <real>] [CUTHA <real>] [VDWR] [IUNIt <int>] - { CONTact } [BRIDge <resnam>] [VERBose] [TCUT real] - 2X(atom-selection) traj-spec - [IRHI <int> [DRH <real> ][RHMAx <real>] ] - [ITHI <int> [DTH <real> ][THMAx <real>] ] - [PBC [CUBIC|TO|RHDO BOXL|XSIZE <real> - [YSIZE <real> [ZSIZE <real>] ] ]] COORdinates SECStructure [first-selection [second-selection]] - [QUIEt | VERBose] [CUTH real] [CUTA real] [STRIct] COORdinates DYNAmics [COMParison] [PAX] [atom-selection] [NOPRint] - traj-spec [ORIENT [MASS] [atom-selection] ] COORdinates PAXAnalysis [COMParison] [atom-selection] [NOPRint] [SAVE] - traj-spec COORdinates SEARch { search-spec } disposition-spec { INVErt } { KEEP xvalue yvalue zvalue } { EXTEnd RBUFf real } search-spec :: [atom-selection] [COMP] [IMAGe] [operation-spec] [XMIN real] [XMAX real] [XGRId integer] [YMIN real] [YMAX real] [YGRId integer] [ZMIN real] [ZMAX real] [ZGRId integer] operation-spec ::= { } { [VACUum] } { [RESEt] } { [RCUT real] } { FILLed } { AND } { [RBUFf real] } { HOLES } { OR } { XOR } { ADD } disposition-spec::= { [NOPRint] } [NOSAve] [CREAte segid CHEM type] {PRINt [UNIT int]} [ SAVE ] COORdinates SURFace [atom-selection] [WEIGhting] { CONTact-area } [ACCUracy real] { ACCEssible-area } [RPRObe real] COORdinates CONVert-from/to-unit-cell [ from | to ] - [atom-selection] [COMP] [IMAGe] - a b c alpha beta gamma [ from | to ] ::= [ FRACtional | SYMMetric | ALIGned ] COORdinates AXIS atom-selection [atom-selection] [MASS] [COMP] [IMAGEs] COORdinates LSQP [ NORM ] [VERBose] [MASS] [COMP] [IMAGEs] [WEIGh] - [ MAJOr ] [ MINOr ] atom-selection COORdinates COVAriance traj-spec 2x(atom_selection) [UNIT_for_output int] - [RESIdue_average_nsets integer] [MATRix] [DIID] - [ENTRopy [TEMP <real>] [DIAG] [RESI] [SCHL] ] - [DCOR|DCOV] COORDinates DMAT - [RESIdue_averaging] [NOE_weighting] [SINGle_coordinate_file] - [CUTOff <real>] [UNIT_for_output <int>] [TRAJectory] [CUTOff <real>] - [PROJect UPRJ <int>] [PROBability UPRB <int>] [TOLE <real>] MKPRoj - traj-spec 2x(atom_selection) [ [RELAtive] RMSF [DUNIt <int>]] [MATRix] COORdinates PUCKer [SEGId segid] RESId resid1 [TO resid2] [AS | CP] COORdinates HELIx atom-selection [atom-selection] COORdinate ANALysis {WATer} [RLP <int>] <atom-selection> - {XREF <real> YREF <real> ZREF <real>} - ! setup arbitrary analysis point {CROSs|SITE [MULTI] <atom-selection>} - ! setup solute analysis site or ! cross terms for arbitrary solvent traj-spec - ! reading trajectories NCORs <int> RSPIn <real> RSPOut <real> - ! MSD/IVAC set-up RSPHere <real> DR <real> MGN <int> - ! g(r) setup RDSP <real> - ! cutoff for DENS,KIRK and DBF DENS <real> - ! userspecified bulk density ! (atoms/A**3) ! for normalization of g(r) {IMSD <unit>|IVAC <unit>} IDENs <unit> - ! output for MSD, VAC and DENsity {IGDISt <unit> [IHH <unit>] [IOH <unit>]|ISDISt <unit>} - ! g(r) requests {BYGRoup|BYREsidue|BYSEgment} ! discard distances WITHIN ! specified unit for g(r) IMRD ! Magnetic Relaxation Dispersion analysis RRES cutoff radius for calculation of residence time. if 0 use shell beteween RSPIN, RSPOUT IKIRkg <unit> - ! Kirkwood g-factor (dipole correlations) RKIRk ! distance dependent Kirkwood factor for water ! iff a SITE MULTI selection containing ! at least two atoms is given, then a unit-vector pointing from the first to the second site atoms will be used in the scalar product with a unit vector along the water dipoles NKIRk number of points in r-dimension for IKIR and RKIR from r=0 to r=RDSP XBOX <real> YBOX <real> ZBOX <real> - !PBC info for analysis IFDBF <unit> IFDT <unit> RCUT <real> ZP0 <real> NZP <int> - ! DBF analysis IHIST <unit> IPDB <unit> [XMIN <real> XMAX <real> DX <real>] - !3D histogram [YMIN <real> YMAX <real> DY <real>] - [ZMIN <real> ZMAX <real> DZ <real>] - [WEIGht] [CHARge] [DIPOle] - [THREshold <real>] [NORM <real>] - IDIP <unit> [MIND <real>] [MAXD <real>] [NUMD <int>] - ! dipole distribution EXVC <atom-selection> MCP <int> MCSH <int> - ! EXcludedVolumeCorrection RPRObe <real> ISEEd [WEIG] - RCOR <integer> - ! Rotational Correlation Time Analysis ROUT <unit> TLOW <real> TUP <real> MAXT <integer> - IHYDn <integer> RHYD <real> ! Hydration numner COORdinates INERtia [atom-selection] - [ENTRopy [TEMPerature <real>] [SIGMa <real>] ] - [STANdard <SOLUtion|GAS>] COORdinates CONFormational { <resname> } [ PRINT ] [ READ io-speficication ] - [atom-selection] [COMP] COORdinates PATH { NREP <int> } {NAME <character*>} [<PDB|FILE|UNFO|CARD|FORM>] COORdinates SMAP {SDENsity} [RESOlution <real>] [RCUT <real>] - [ORIENT [<MASS|WMAIn>] [NORO]] atom-selection - IUNW <integer> traj-spec [<EMAP|CARD>] - [SOLV OH2] ! Options for SDEN also apply for DIFT and HBON {DIFTrans} [DCUT <real>] [HCUT <real>] [WDISt <real>] - [IDIF <integer>] {HBONd} [ISLT <integer>] [ISLV <integer>] - [ITOT <integer>] [CUTH <real>] [DCUT <real>] atom-selection:== (see select .) distance-spec::= { WEIGhting vector-spec atom-selection } { } { [UNIT int] [CUT real] [ENERGy [CLOSe]] 2X(atom-selection) - } { [Nonbonds] } { [NO14exclusions] } { [NOEXclusions] } - { NONOnbonds } { 14EXclusions } { EXCLusions } [TRIAngle] [ HISTogram HMIN real HMAX real HNUM integer - [HSAVe] [HPRInt] [HNORm real] [HDENsity real] ] vector-spec::= { [XDIR real] [YDIR real] [ZDIR real] } [DISTance real] [XCEN real] [YCEN real] [ZCEN real] [FACTor real] { AXIS } draw-spec::= [DFACt real] [NOMO] UNIT integer io-specification:== (see io .) traj-spec::= [FIRSt int] [NUNIts int] [NSKIp int] [BEGIn int] [STOP int]
Top Descriptions of the simple coordinate manipulation commands All of these commands allow either the main coordinate set (default), or the comparison set (COMP keyword) to be modified. The other coordinate set is only changed by the SWAP command and the ORIEnt RMS command when the specified atoms are not centered about the origin. The DIMS coordinate set (DIMS keyword) is used with the DIMS command (*note DIMS:(dims.doc).) and it is mainly used with COPY to load the target structure: 'COOR COPY DIMS'. The DIMS set also works with ORIENT, PRINT, and STAT, but not with any other operations. Copy the DIMS set to the comparison set ('COOR COPY DIMS COMP') if other operations on the target structure are required. Each of these commands may also operate on a subset of the full atom space. The selection specification should be at the end of the command. The default atom selection includes all atoms. If the IMAGes keyword is specified, then the operation will be performed on the image atoms as well (if images are present). The SECOnd keyword specifies that the second comparison set be used. This keyword can be used with any command that uses a comparison set (e.g. COPY COOR COMP SECOnd to copy coordinates to the second comparison set; COPY COOR SECOnd to copy the coordinates from the second to the main set). Use of this command requires compilation with the COMP2 precompiler keyword. ------------------------------------------------------------------------------ 1) The INITialize command The INITialize command returns the coordinate values of the specified atoms to their start up values (9999.0). The main use of this command is in connection with the IC BUILD command, which may only find coordinates for atoms with the initial value. ------------------------------------------------------------------------------ 2) The COPY command The COPY command will copy the coordinate values into the specified set FROM the other coordinate set. ------------------------------------------------------------------------------ 3) The SWAP command The SWAP command will cause the coordinate values of the specified atoms to be swapped with the comparison set. ------------------------------------------------------------------------------ 4) the AVERage command The AVERage command will generate a new coordinate set at a point along the displacement vector between the present coordinate set and the other set. The FACTor value determines the relative step along this vector. Its default value is 0.5 (a true average). A FACTor value of 1.0 is equivalent to the copy command. Negative or greater than unit positive values are also allowed. ------------------------------------------------------------------------------ 5) The SCALe command The SCALe command will cause the coordinate values for all selected values to be scaled by a required scale factor. This option is designed to work with coordinate displacement vectors. A scale factor of zero will set the selected coordinate values to zero. This option may also be useful in plotting. ------------------------------------------------------------------------------ 6) The MASS_weighting command The MASS_weighting command will cause all selected coordinates to be scaled by the MASS of each atom. If the WEIGht option is specified, the weighting array will be scaled. ------------------------------------------------------------------------------ 7) The ADD command The add command will add the main and the comparison coordinate values and store the results in the selected coordinate set. As with other commands, only selected atoms will be modified. If an atom in either set is undefined, then the sum will also be undefined. This option is designed for use in cases where one or both coordinate sets contain coordinate displacement vectors. ------------------------------------------------------------------------------ 8) The SET command The SET command will set all coordinate values of selected atoms to a specified value determined by the vector specified. This is a simple manner in which to zero a coordinate set with the command; COOR SET XDIR 1.0 DIST 0.0 Note, the XDIR keyword value was included so that the vector has a nonzero norm (required for all vector specifications). ------------------------------------------------------------------------------ 9) The TRANslate command The TRANslate command will cause the coordinate values of the specified atoms to be translated. The translation step may be specified by either X,Y, and Z displacements, or by a distance along the specified vector. When no distance is specified, The XDIR,YDIR, and ZDIR values will be the step vector. If the AXIS keyword is used, then the translation will be along the axis defined by the previous COOR AXIS command. For this option, a distance may be specified, but if it isn't, then the translation distance will be the COOR AXIS vector length ------------------------------------------------------------------------------ 10) The ROTAte command The ROTAte command will cause the specified atoms to be rotated about the specified axis vector through the specified center. The vector need not be normalized, but it must have a non-zero length. If the AXIS keyword is used, then the axis and center information from the last COORdinates AXIS command will be used. The PHI value gives the amount of rotation about this axis in degrees. Only the atoms specified will be rotated. If the MATRix keyword is used the rotation will be made using an explicit rotation matrix, input in free format on the three following lines (3 real numbers /line): U(1,1) U(1,2) U(1,3) U(2,1) U(2,2) U(2,3) U(3,1) U(3,2) U(3,3) NOTE: This command uses a LEFT HAND sense, not the usual right hand rule... It was a mistake, but this is kept for historical reasons (numerous scripts). The left hand sense is consistent with dihedral angles (i.e. if you define a vector along bond A-B (from A to B) and then rotate B (and its bonds) by a positive angle (in the left hand sense), then the dihedral angles will increase. Other rotation angles in CHARMM (should) use the regular right hand rule (except for the COOR TWISt command). ------------------------------------------------------------------------------ 10.5) The TWISt command The TWISt command will cause the specified atoms to be rotated about the specified axis vector through the specified center. The vector need not be normalized, but it must have a non-zero length. If the AXIS keyword is used, then the axis and center information from the last COORdinates AXIS command will be used. The amount of rotation will depend on the projected distance of the atom on the axis multiplied by the RATE value (in degrees). This command was designed to generate helical structures that are more or less twisted than an initial helical structure. This is an easy way to homogeneously perturb a helix. I can be also used to induce a twist in planar structures. NOTE: this command uses a left handed sense, not the usual right hand rule... (see ROTAte above). ------------------------------------------------------------------------------ 11) The ORIEnt command The ORIEnt command will modify the coordinate values of ALL of the atoms. The select set of atoms is first centered about the origin, and then rotated to either align with the axis, or the other coordinate set. The RMS keyword will use the other coordinate set as a rotation reference. The MASS keyword cause a mass weighting to be done. This will align the specified atoms along their moments of inertia. When the RMS keyword is not used, then the structure is rotated so that its principle geometric axis coincides with the X-axis and the next largest coincides with the Y-axis. This command is primarily used for preparing a structure for graphics and viewing. It can also be used for finding RMS differences, and in conjunction with the vibrational analysis. The NOROtation keyword will suppress rotations. In this case, only one coordinate set will be modified. ------------------------------------------------------------------------------ 12) The RMS command The RMS command will compute the RMS or mass weighted RMS coordinate differences between the selected set of atoms just as they lie. This differences from the COOR ORIENT RMS command in that no coordinate modifications are made and no translation is done. ------------------------------------------------------------------------------ 13) The DIFF command The DIFF command will compute the differences between the main and comparison set (or the reverse) and store this difference in the modified coordinate set. Undefined or unselected atoms result in a zero. If the WEIGht keyword is invoked, then the WCOMP array is subtracted from WMAIN and the coordinates are untouched. ------------------------------------------------------------------------------ 14) The FORCe command The FORCe command will copy the current forces (DX,DY,DZ) of the selected atoms to the specified coordinate set. Atoms not selected are given a value of zero. If the MASS keyword is specified, then the forces will be divided by the mass. This would correspond to an acceleration in dynamics. ------------------------------------------------------------------------------ 15) The SHAKe command This command will SHAKE the selected coordinate set with respect to the other (as a reference). A mass weighting may be used. Any atoms that are not selected are considered to be fixed (infinite mass). In order to use this command, the SHAKe command must first be invoked which sets up the shake constraints. Lone pairs (lonepair.doc) with undefined coordinates can be built by COOR SHAKE. ------------------------------------------------------------------------------ 16) The DIPOle command Calculates the dipole moment of selected atoms. If total charge is not zero, the dipole moment is somewhat ill-defined and coordinate system dependent; in this case the center of geometry of the selected atoms is used as origin for the coordinate system in which the dipole moment is calculated. This can be altered by the MASS keyword. If it is present the center of mass will be used as origin of the relative coordinate system. For the purpose of compatibility with Gaussian program this feature can be disabled by adding OXYZ keyword, which forces calculation of dipole moment relatively to the origin of Cartesian coordinate system. Prints out dipole moment cartesian components and magnitude (in Debyes) and the total charge. CHARMM variables ?CHARGE, ?XDIP, ?YDIP, ?ZDIP, and ?RDIP (charge, x,y,z and magnitude of dipole) are set. ------------------------------------------------------------------------------ 17) The UFSR command Compare two structures (working set versus comparison set) with the Ultra Fast Shape Recognition algorithm by Ballester and Richards (*note Ballester 2007:(chmdoc/dims.doc)References.). This algorithm is intended to differentiate two structures based on atomic distributions. Notice that in this approach the score is normalized and a value of 1 means two identical structures. The current implementation is identical to the one proposed in their paper.
Top Descriptions of the remaining corman commands See the descriptions of the simple commands for some background information on these commands. ------------------------------------------------------------------------------ 1) The DISTance command The COOR DIST command will either find distances between atoms or the distances of atoms from a fixed point in space (WEIGh option). This command can find distances within a single coordinate set, or find distances between atoms in two coordinate sets (DIFF option). The DISTance command can find all atom distances between two atom selections. A unit number may be specified (default=6) and a cutoff distance may be included as well (default=8999.0). If no selection is specified, all atoms will be included! The delimiter ENDselection must separate the two sets of atom selections. The van der Waal energy may be requested with the "ENERgy" keyword, and if this option is used, the list of pairs with a positive van der Waal energy may be selected with the "CLOSe" keyword (i.e. only close contacts will be listed). The NEAR option will list the nearest atom in the second atom selection to the atoms in the first selection. The COOR DISTance command doesn't gives distances between excluded atoms unless the "EXCLusions" keyword is specified. This make it much easier to search for bad contacts. Likewise, 1-4 interactions and other interactions may be requested or omitted. The command; COOR DISTance ENERgy CLOSe CUT 5.0 SELE ALL END SELE ALL END - 14EXclusions NONBonds will list all atom pairs that have a positive van der Waal energy. The command; COOR DISTance ENERGY CUT 5.0 NONONbonds NOEXclusions 14EXCLusions - SELE ALL END SELE ALL END will list all 1-4 interactions and energies (and nothing else). The command; COOR DISTance ENERgy CUT 4.5 SELE RESID 23 END SELE ALL END will list all contacts less than 4.5A that residue 23 has with the rest of the system without considering 1-4 interactions or excluded pairs. The 1-4 vdw terms, E14FAC, and EPS values other than 1.0 are recognized. The WEIGht option puts the distance of all selected atoms from some specified point. If no point is specified, then the origin is used. This is most useful in computing magnitudes of forces or coordinate differences. For example, the sequence; ENERGY ... COOR FORCE COMP ! copy forces to the comparison coordinates COOR DIST WEIGH COMP ! put magnitudes in the weighting array. PRINT COOR COMP SELE PROP WCOMP .GT. 5.0 END ! print atoms with large forces. Note that all operations were done on the comparison set. The DIFF keyword causes the selection to work on different coordinate sets, where the first selection corresponds to the set specified (MAIN or COMP), and the second atom selection uses the other coordinate set. The HISTogram option allows a histogram of distances to be produced. With the histogram, the HMIN and HMAX (the range of the histogram in angstroms) and the HNUM (the number of bins) must be specified. The HSAVe keyword causes the histogram values to be saved for subsequent COOR DIST commands. In a loop, this allows g(r) to be calculated from a dynamics trajectory. The HPRInt option will cause the final histogram values to be printed. The HNORm value will be used to normalize the histogram before printing (divide by HNORm). A density value, HDENS, is also required, which is the number of selected objects divided by the volume per object. Also note: In order to get this to work with with the crystal facility, the first atom selection (in the loop) should only include primary atoms, and the second atom selection should include both primary and image atoms. The histogram will be scaled by the reciprocal of the distance squared The histogram will also be scaled by the reciprocal of the distance squared (to get normalized g(r) plots). Three columns of numbers are output; (1) the bin midpoint distance, (2) the normalized g(r), and (3) the total number of pairs within the bin divided by the HNORM value. A PRNLEV less than 5 will suppress the listing of distance pairs. Example of use to get a distance distribution plot: update imgfrq 20 cutim 20.0 traj .... prnlev 4 set 1 1 label loop traj read update inbf 0 IMALL cutim 10.5 coor dist image sele segid main .and. type OH2 end sele type OH2 end - cut 10.5 HIST HMIN 0.0 HMAX 10.0 HNUM 50 HSAVE incr 1 by 1 if 1 .lt. 1000.5 goto loop calc dens = 216.0/30.0 ! #waters/(volume/water) coor dist sele none end sele none end - cut 10.5 HIST HMIN 0.0 HMAX 10.0 HNUM 50 HNORM 1000.0 - HPRINT HDENS @dens COOR DIST RESI calculates residue-to-residue minimum distances between two selections. This is useful when analyzing long simulation trajectories where printing out atom-to-atom distances at each frame generates too much data to handle, whereas the first-hand interests are identifying residues that make contact. Minimum distance between each pair of residues from two atom selections is calculated and printed if PRNLEV >=4. Only distances less than CUT are considered. Also, distances are calculated only between different residues. For a single selection, if residues within the same segment are compared, distances are printed only for pairs where the RESID of the first residue is less than that of the second residue. This avoids printing the same information twice. The number of distance pairs identified is set to the variable NPAIR. As an example, to find nonpolar contacts between two selections, one can do: DEFI A1 SELE ( SEGI A .AND. (PROP ABS CHARGE .LT. 0.30)) END DEFI A2 SELE ( SEGI B .AND. (PROP ABS CHARGE .LT. 0.30)) END COOR DIST RESI CUT 3.0 SELE A1 END SELE A2 END To find all internal nonpolar contacts, use a single atom selection: COOR DIST RESI CUT 3.0 SELE A1 END ------------------------------------------------------------------------------ 2) The RGYR command The RGYR command can compute the Radius of GYRation, center-of-mass and total mass of the specified atoms. By default the RGYR, uses a unit weighting factor providing the rms distance from the center of geometry. The current keywords are: MASS use mass weighting (otherwise use unit weight per selected atom) WEIG use a weight array (WMAIN or WCOMP) for the weighting FACT constant to be subtracted from each weight The weight arrays can be filled, by using COOR or SCALAR commands, before invoking the RGYR routine. In this way almost any RGYR can be computed. ------------------------------------------------------------------------------ 3) The LSQP command The LSQP command computes the least-squares-plane through the selected atoms. Weighting can be done by the atom masses [MASS], by the weighting array [WEIG], or not at all (default). Output is the equation for the plane, the sum-of-squared distances (weighted) from the plane (SSQ), and the center-of-mass of the selected atoms. The keyword VERBose causes some additional output, most useful of which is the distance from the plane for each atom. The options; NORM, MAJOr, and MINOr select which vector is stored as the AXIS (see COOR AXIS command for more details). The default is to not set the AXIS variables. ------------------------------------------------------------------------------ 4) The OPERate command. The OPERate command processes the selected coordinates through the image transformation specified by name. This command may only be used if an image file has been read. The image_name is one of the image transformation names (WRITE IMAGE TRANS). This is also the SEGID of the image atoms created by the image update procedure. ------------------------------------------------------------------------------ 5) The MINDistance command. The MINDistance command computes the minimum distance between selected coordinates. Usually this command is executed with a double selection. Note that the default distance-spec excludes bonded atoms and 1-4 interactions. If only one selection is given, then it will give the minimum distance of the selected coordinates between the MAIN and COMPARISON set. ------------------------------------------------------------------------------ 6) The MAXDistance command. The MAXDistance command computes the maximum distance between selected coordinates. This command is executed with a double selection. ------------------------------------------------------------------------------ 7) The STATistics command The STATistics command will print some simple statistics regarding the selected atoms. The values XMIN,YMAX,XAVE,YMIN,YMAX,YAVE, ZMIN,ZMAX,ZAVE,WMIN,WMAX,WAVE are set when this command is executed. These variable values may then be used un subsequent commands with the "?" symbol. For example, the command sequence may be used to shift a structure so that a single atom is in the X-Y plane (e.g. shift in the z-direction); COOR STATistics SELE desired-atom END COOR TRANS ZDIR ?ZAVE FACT -1.0 The MASS option will place the average values at the center of mass. ------------------------------------------------------------------------------ 8) The AXIS command. The AXIS command generates a vector and saves it for subsequent use for either command parsing, or for use as input in the COOR SET, COOR ROTAte, COOR TRANslate, or COOR DISTance WEIGhting commands by using the AXIS keyword. There are two modes for the AXIS command. With a single atom selection, the stored vector is the defined from the origin to the center of geometry/mass of all selected atoms. With two atom selections, the vector spans from the center of the first set of selected atoms to the center of the second. The MASS keyword invokes the usage of the center of mass. The AXIS command sets the variables XAXIs, YAXIs, ZAXIs, RAXIs, XCEN, YCEN, and ZCEN, which may be accessed with the "?" symbol. These values define the actual vector, the length of the vector, and the center of the vector (midpoint). For example, to use the distance between two atoms as a criterion to terminating a run, the following command sequence could be used; SET 1 10.0 COOR AXIS SELE first-atom END SELE second-atom END IF 1 GT ?RAXIs STOP For another example, to rotate the chi-1 torsion of a specified residue BY 30 degrees, the command sequence would be appropriate; DEFINE BACK SELE TYPE O .OR. TYPE N .OR. TYPE H .OR. TYPE CA .OR. TYPE C END COOR AXIS SELE ATOM MAIN 23 CA END SELE MAIN 23 CB END COOR ROTATE AXIS PHI 30.0 SELE RESID 23 .AND. .NOT. BACK END ------------------------------------------------------------------------------ 9) The DUPLicate command. The DUPLicate command copies coordinates between atoms within a structure. The coordinates are copied FROM the first selection TO the second selection. If the selections overlap, watch out!. The matching is done by number within the selected coordinate sets. If the two selection have a different number of atoms, a warning will be issued, and the smaller number will be used. For example, if one needs to compute the relative orientation between two alpha helicies, the following input might be used; COOR COPY COMP COOR DUPL COMP SELE backbone of first END SELE backbone of second END COOR ORIE RMS MASS COMP SELE backbone of second END This will give the RMS shift between these helicies as well as the coordinate transformation required to map one into the other. The PREVious option may be used with a single atom selection. This assigns the coordinate position of selected atoms to the value of the previous atom (by number). This has been used with the command; COOR DUPLicate PREVious SELE TYPE H* END to assign hydrogen atom positions to that of the associated heavy atom. The COMP keyword causes only the comparison coordinates to be used and modified. Otherwise, the entire operation involves only the main coordinates. ------------------------------------------------------------------------------ 10) The DYNAmics command The COOR DYNAmics command will read a (set of) dynamics trajectory files and compute the average coordinates (stored in the selected coordinate set) and the isotropic rms fluctuations (stored in the weighting array). The first unit number (FIRSt)(default 51), number of units (NUNIts) (default 1), frequency of accepted coordinate sets (NSKIp)(default 1), starting set (BEGIn)(default first set), last set (STOP)(default last set), may be specified. Option values are not remembered with subsequent COOR DYNA commands. The NOPRint supresses much of the output. If the keyword ORIENT is present, all coordinate frames will be RMS re-oriented with respect to the COMParison set (must be defined); if the word MASS is also there the coordinates will be mass-weigthed for re-orientation; if a second atom selection is provided, only those selected atoms will be used. The PAX command causes the Principal AXis of the motion of each atom to be computed and save. The print out gives the direction and magnitude of the fluctuation as well as the anisotropies. The PAX data is saved for a subsequent COOR PAXAnal command if further analysis is desired. ------------------------------------------------------------------------------ 11) the PAXAnal command The COOR PAXAnal command computes additional data regarding the Pricipal AXis data (computed by the most recent COOR DYNA PAX command). The trajectory must be reopened and reread, or a different trajectory may be substituted. This command prints data for each selected atom and averages over the selected atoms. The printout includes the skew and kurtosis, anisotropies, as well as all of the low moments of the motion. The SAVE option causes the PAX data structure (from the COOR DYNA PAX command) to be saved (for subsequent COOR PAXA commands). ------------------------------------------------------------------------------ 12) the SEARch command COORdinates SEARch { search-spec } disposition-spec { INVErt } { KEEP xvalue yvalue zvalue } { EXTEnd RBUFf real } search-spec :: [atom-selection] [COMP] [IMAGe] [operation-spec] [XMIN real] [XMAX real] [XGRId integer] [YMIN real] [YMAX real] [YGRId integer] [ZMIN real] [ZMAX real] [ZGRId integer] operation-spec ::= { } { [VACUum] } { [RESEt] } { [RCUT real] } { FILLed } { AND } { [RBUFf real] } { HOLES } { OR } { XOR } { ADD } disposition-spec::= { [NOPRint] } [NOSAve] [CREAte segid CHEM type] {PRINt [UNIT int]} [ SAVE ] The SEARch command generates and/or manipulates a grid of small volume elements. The SEARch command will search through a set of grid points for vacuum space points (i.e. points outside the van der Waal radius of any atom). In the default mode (NOPRint), only the relative volume of filled and vacuum points are printed concerning the selected atoms. The grid specifiers must be input (min, max, and grid) for each dimension. (grid implies number of grid points. Hence XMIN -10.0 XMAX 10.0 XGRID 41 implies a half Angstrom sampling along the x direction) The FILLed option will cause non-vacuum points to be listed or plotted. The PRINt option will cause all found grid points to be listed on the output unit specified (default 6). For this command, the atom sizes (radii) are taken from the weighting array. To get van der Waal radii into the weighting array, the command; SCALar WMAIn = RADIus may be used. If a hole big enough to stuff a water into is to be found, then the command sequence; SCALar WMAIn = RADIus SCALAR WMAIN ADD 1.6 SCALAR WMAIN MULT 0.85 would be probably the best to use. If the RCUT or RBUFf value is set to a nonzero value, then the accessible volume command is enabled. When RCUT is set, this is the maximum radius. When RBUFf is set, then the maximum radius is the weighting array plus the RBUFf value. The weighting array is returned with the fraction of free volume in the shell from the atom radius to the maximum radius. If the HOLEs keyword is set, only the grid points not connected to the first point (point in the negative corner of the box) are considered. In this way, the volume of just the holes can be analyzed and saved. The "ADD" option for the COOR SEARCH command has been added to allow the calculation of partial occupancy factors. This allow holes in proteins to be analyzed for flexibility and variability. It is possilbe to use multiple COOR SEARch commands and to use boolean operations to combine the results. For example, the script sequence; COORdinates SEARch IMAGe - XMIN -10.0 XMAX 10.0 XGRId 20 - YMIN -10.0 YMAX 10.0 YGRId 20 - ZMIN -10.0 ZMAX 10.0 ZGRId 20 - NOPRINT VACUUM SAVE .... SCALAR WMAIN ... .... COORdinates SEARch IMAGe - XMIN -10.0 XMAX 10.0 XGRId 20 - YMIN -10.0 YMAX 10.0 YGRId 20 - ZMIN -10.0 ZMAX 10.0 ZGRId 20 - AND PRINT UNIT 22 RBUFF 2.0 FILLED NOSAVE Note, the results of these two commands are computed and the intersection (AND) is printed. The first command needs a "SAVE" in order for the results to be saved. Also, the grids (if specified) must exactly match (same number of grid points in all dimensions) for this operation to work. The COOR SEARch command allocates space, if needed, and frees the space when the NOSAve option is used. Thus, if four COOR SEARch commands are needed for a single computation, the first must have the SAVE option. The only way to free the space allocated by the COOR SEARch SAVE command is to run another COOR SEARch command with the NOSAve option. If the CREAte option is used then the specified grid points will be added to the PSF as dummy atoms. The chemical type of the dummy atom must be specified and it must be present in the current RTF. This option can be used for graphics or for other hole analysis (shape,...). This option will add one segment to the PSF, one residue and atoms and groups equal to the number of selected grid points. ------------------------------------------------------------------------------ 13) the VOLUme command The VOLUme command will compute the volume of a selected set of atoms. Its operation is the same as that of the SEARch command, except that only the volume is printed and the degree of exposure for each atom is returned in the weighting array. The SCALAR storage arrays must be filled before using this command. The first storage array [1] must contain the radii of each atom (RMIN) and the second storage array must contain the outer probe distance (RMAX) for each atom. The free volume within the RMIN to RMAX range and not within RMIN of any other atom will be returned in the weighting array as a ratio of the maximum possible value. For example a completely exposed atom will return a value of 1.0 and an atom in the interior of a protein would return a value of 0.0. The HOLEs keyword feature causes holes within the selected atoms to be filled before computing the total volume and the accesible volume. SPACE is a maximum number of cubic pixels i.e. SPACE = x_points * y_points * z_points Larger SPACE value results in more accurate calculation but it takes more memory an computer time. Number of points in x,y and z directions are determined according to the formula: factor = ( SPACE / (a*b*c) ) ** (1/3) x_points = factor*a y_points = factor*b z_points = factor*c where a, b and c are dimensions of the smallest rectangular box enclosing the molecule. ------------------------------------------------------------------------------ 14) The SURFace command The COOR SURFace command computes the Lee and Richards surface for selected atoms and stores the result in the appropriate weighting array. If the "WEIGhting" keyword is used, the radii are obtained from the weighting array (and then written over), otherwise the radii are obtained from the parameter file values. The radius of the probe may be specified (default 1.6) and the accuracy may be specified (default 0.05). Either ACCEssible surface (default) or CONTact surface may be specified. Contact surface is equivalent to Accessible surface if a zero probe radius is used. If the accuracy is not specified (or set to zero), then the analytic result is provided. If a nonzero accuracy is provided, then the original Lee and Richard's (points on a sphere) algorithm is used. ------------------------------------------------------------------------------ 15) The HELIX command The COOR HELIx command will analyze a single helix, or the relative orientation of two helices. The use this command, one or two atom selections should be provided selecting ONLY the atoms which will be used to define the helix. The order of these atoms is important. With a single atom selection, this command calculates the normalized axis (A) and the perpendicular vector (R0) from the origin to A of the cylinder most closely approximating a helix on which the selected atoms best fit (Algorithm by J. Aqvist Computers & Chemistry Vol. 10, pp97-99, (1986)). With a double atom selection, this command also computes helix axis and helix-helix structure analysis (Algorithm by Chotia, Levitt, and Richardson JMB 145, P215-250 (1981)). ------------------------------------------------------------------------------ 16) The CONVert command The COOR CONVert command will cause the coordinates of all defined and selected atoms to be transformed from the unit cell to cartesian coordinates or back from cartesian to fractional coordinates. Two orientations in cartesian coordinates are supported : ALIGned - in which b-vector is along y-axis and a-vector in xy-plane (this is old charmm standard) SYMMetric - in which shape matrix constructed from unit cell vectors is symmetric Two keywords in any order [FRAC|ALIG|SYMM] are required after CONVert. Unit cell parameters (a,b,c,alpha,beta,gamma) follow in the same line. The angle values are specified in degrees. See the routine CONCOR for details concerning the transformation. As an example, the following manipulations should have no net affect on the coordinates, COOR COPY COMP COOR CONVERT SYMMETRIC FRACTIONAL 5.6 12.2 5.4 80.0 95. 100. COOR CONVERT FRACTIONAL SYMMETRIC 5.6 12.2 5.4 80.0 95. 100. COOR CONVERT SYMMETRIC ALIGNED 5.6 12.2 5.4 80.0 95. 100. COOR CONVERT ALIGNED FRACTIONAL 5.6 12.2 5.4 80.0 95. 100. COOR CONVERT FRACTIONAL ALIGNED 5.6 12.2 5.4 80.0 95. 100. COOR CONVERT ALIGNED SYMMETRIC 5.6 12.2 5.4 80.0 95. 100. COOR DIFF COOR STAT When working with a triclinic system, the user should be aware of the form of the coordinates. Most of the data from crystallography is in fractional (coordinates between zero and one) or in the aligned frame. NOTE: All of the internal use in CHARMM for energy calls, minimization, or dynamics ASSUMES that the coordinates are in the symmetric frame. ------------------------------------------------------------------------------ 17) The COVAriance command The covariance command under coordinate manipulations computes covariances of the spatial atom displacements of a dynamics trajectory for selected pairs of atoms. mu = E[ (R - E[R ]) (R - E[R ] ) JK J J K K = E[R R ] - E[R ] E[R ] J K J K and the normalized covariance matrix is given by CO = mu / SQRT(mu mu ) JK JK JJ KK The command syntax and varibles are as in the coor dynamics command. The exceptions are the keywords: SET1: specifies the selection for the "J" groups in covariance SET2: specifies the selection for the "K" groups in covariance UNIT_for_output: specifies unit for output of covarience matrix (ascii) RESIdue_average: is a logical for computing the average over residues in SET2 specification. When followed by NSETS: equal to 2 the average is over both SET1 and SET2 giving a NRES1 x NRES2 covariance matrix. MATRix gives output of just the covariance values in a matrix format DIID: generates covariance matrix calculated with respect to COMP coordinates instead of the average conformation from within the trajectory. Useful for DIRECT-ID analysis. See Lakkaraju et al, JCC, doi:10.1002/jcc.24231 for method details. ENTRopy config. entropy [kcal/mol/K] using approximation S'' of Andricioaei&Karplus (J. Chem. Phys 115,6289 (2001)) or SCHL J. Schlitter's variation S' (Chem. Phys. Lett. 215, 617 (1993)) on Karplus&Kushick. See also Schafer et al J. Chem. Phys. 113, 7809 (2000). This approximation is an upper limit to the true entropy. Sets CHARMM variable ENTROPY It is recommended to remove translational(rotational) motion before extracting the entropy (merge orient..[norot].); for flexible molecules removal of rotation may be tricky. NB! The covariance matrix used for this calculation is not normalized and is 3N by 3N TEMP temperature used in entropy calculation (default 298.15) DIAG use only diagonal elements of covariance matrix, mainly for testing purposes RESI evaluate entropy using covariance for each residue only DCOR|DCOV calculate distance correlation (covariance) between positional fluctuation of two selection of atoms. See dcor.doc Example: !Get configurational entropy at T=300K and save the unnormalized covariance !matrix, using all atoms in the PSF coor cova firstu 51 nunit 1 entropy matrix unit 61 temp 300.0 ! Same without saving or printing the matrix and with output for each residue coor cova firstu 51 nunit 1 entropy unit -1 temp 300.0 resi ------------------------------------------------------------------------------ 18) The DMAT command This command is accessed with the command COOR DMAT and provides some general tools for the calculation, manipulation and storage/extraction of distance matrix based properties. This routine has some overlap with the new distance command introduced by Bernie Brooks but also provides significant complementarity in extending the range of properties computed. The entire syntax is: [SYNTAX] COORdinates DMAT - RESIdue_average NOE_weighting - SINGle - FIRSt_unit <int> NUNIt <int> BEGIn <int> SKIP <int> - STOP <int> 2x<atom selection (SET1, SET2)> - UNIT_for_output <int> TRAJectory CUTOff <real> - PROJect UPRJ <int> [MKPRoj] PROBability UPRB <int> TOLE <real> - [ [RELAtive] RMSF] [DUNIt <int>] [MATRix] The command structure is like that of most other coordinate manipulation commands other sub-parser keywords are: UNIT the distance matrix will be written to the unit number specified as an ASCII file unless the TRAJ keyword is specified, in which case a binary "trajectory" of the distance matrix will be written. RESIdue this keyword specifies to compute the distance matrix for a center of geometry weighted average of residues NOE this keyword denotes that the averaging over distances in the distance matrix should be inverse sixth power weighted. TRAJ write a dynamic trajectory file of the distance matrix SINGle process only a single coordinate file CUTOff print only those values of the distance matrix which are smaller than cutoff value PROJect project out a subset of contacts for printing UPRJ read projection matrix from unit UPRJ MKPRoj A projection matrix will be printed. Its elements are 1 if the distance is < CUTOff, 0 otherwise. To be used with subsequent PROJ UPRJ unit command. (If a standard DMAT is used as projection matrix the CUTOff in the PROJ command has to be squared) PROB compute the contact probability based on differences from reference contact map read from UPRB and with an upperbound tolerance of TOLE RMSF Computes the root mean square fluctuation in the distance matrix from the trajectory. Disables the printing of the binary file. RELAtive Divides the RMSF value by the distance DUNIt Write distances to file open on the specified unit. This allows calculation of distance and (relative) fluctuation matrices in one pass. MATRix Output is in the form of a rectangular matrix with just the z-values (distances or fluctuations) Note: The binary file produced is analogous to the binary trajectory files and contain the following information: WRITE(UNIT) HDRD,ICNTRL CALL WRTITL(TITLEA,NTITLA,UNIT,-1) WRITE(UNIT) NSET1,NSET2 WRITE(UNIT) (IND1(I1),I1=1,NSET1) WRITE(UNIT) (IND2(I2),I2=1,NSET2) and then nframes of WRITE(UNIT) ((CO(I1,I2),I1=1,NRES1),I2=1,NRES2) Where ICNTRL is a 20 element integer array with the following data: ENDDO ICNTRL(1) = (STOP - BEGIN)/SKIP ICNTRL(2) = BEGIN ICNTRL(3) = SKIP ICNTRL(4) = STOP - BEGIN ICNTRL(5) = NSAV ICNTRL(8) = NDEGF ICNTRL(9) = NATOM - NFREAT CALL ASS4(ICNTRL(10),SKIP*DELTA) IF(LNOE) THEN ICNTRL(11) = 1 ELSE ICNTRL(11) = 0 ENDIF IF(LRESI) THEN ICNTRL(12) = 1 ELSE ICNTRL(12) = 0 ENDIF and NSET1[2] are the number of atoms comprising the two selections and IND1[2](NSET1[2]). The distance matrix CO(NRES1,NRES2) is a 2-D array of size either NSET1 x NSET2 or NRES(NSET1) x NRES(NSET2) depending on whether the residue flag was used in processing the commands Examples of usage: ------------------ 1. Compute the distance matrix for a single coordinate file (resident in the main coordinate set) and print this matrix to a file linked to fortran unit 1. open unit 1 write form name total.dmat COOR DMAT SINGLE UNIT 1 SELE ALL END SELE ALL END 2. Compute the side chain-side chain center of geometry distance map from a single coordinate file and print the distanice matrix to unit 1 zeroing all elements of the matrix with distances greater than 6.5 angstroms define bb select ( type ca .or. type n .or. type c .or. typ o ) end define side select ( (.not. bb) .and. (.not. hydrogen) ) end open unit 1 write form name side.dmat coor dmat residue_average single unit 1 cutoff 6.5 select side end - select side end 3. Compute the average hydrogen atom-hydrogen atom distance map from a trajectory file on unit 10 and print the average distance matrix to unit 1. Use NOE inverse-sixth power weighting in the averaging and "filter-out" all distances in the final map with values greater than 6.0 angstroms. open unit 10 read unform name trajectory.crd open unit 1 write form name noe.dmat coor dmat unit 1 cutoff 6.0 noe_weighting select hydrogen end - select hydrogen end - first_unit 10 nunit 1 begin 100 skip 100 stop 10000 4. Compute the center-of-gemoetry distance matrix for side chains and write this as a binary "trajectory" file to unit 1. Read the trajectory from unit 10. open unit 10 read unform name trajectory.crd open unit 1 write unform name side.dm-trj define bb select ( type ca .or. type n .or. type c .or. typ o ) end define side select ( (.not. bb) .and. (.not. hydrogen) ) end coor dmat residue_average unit 1 traj select side end select side end - first_unit 10 nunit 1 begin 100 skip 100 stop 10000 5. Compute the center-of-geometry contact map probability based on a precomputed distance matrix (e.g. from a PDB structure) based on a 6.5 A cutoff. (This example is for the interdomain (helix-helix) contacts in GCN4. The two helices are segids zipa and zipb.) ! First contacts open unit 1 read unform name "traj/crdp/2zta/2zta_d1-60p.crd" ! trajectory file to use to compute probability from open unit 2 write form name "distance_matrix/2zta_d1-60p.dmatp" ! file to write contact probability matrix to open unit 3 read form name "distance_matrix/2zta_full.dmat ! reference contact map coordinates dmat residue unit 2 - first 1 nunit 1 begin 100 skip 100 stop 600000 - select side .and. ( segid zipa ) end - select side .and. ( segid zipb ) end - probability uprb 3 tole 0.3 cutoff 6.5 close unit 1 close unit 2 close unit 3 6. The following example shows the use of the dmat command to count the number of contacts (native and non-native) throughout the course of a trajectory using the distance matrix projection operator and the fact that the number of contacts are accessible through the ?ncontact variable. label dotraj ! Now we loop over the trajectory and compute time dependent properties open unit 1 read unform name "traj/crdp/2zta/2zta_d1-60p.crd" open unit 10 write form name "distance_matrix/2zta_d1-60p.traj" write title unit 10 *# Properties for Contacts *# trajectory 2zta_d1-60p. *# time(ps) C(native) C(total) traj iread 1 nread 1 begin 500 skip 500 stop 600000 set time 1.0 set frame 1 label loop trajectory read ! First get the contact information open unit 3 read form name "distance_matrix/2zta_full.dmatp" ! reference distance matrix to use for projection open unit 2 write form name "distance_matrix/temp.dmat" ! junk distance matrix coor dmat single residue unit 2 cutoff 6.5 - select ( side .and. segid zipa ) end - select ( side .and. segid zipb ) end - proj uprj 3 set cnat ?ncontact open unit 2 write form name "distance_matrix/temp.dmat" coor dmat single residue unit 2 cutoff 6.5 - select ( side .and. segid zipa ) end - select ( side .and. segid zipb ) end set ctot ?ncontact ! Write information to file write title unit 10 * @time @cnat @ctot incr time by 1.0 incr frame by 1 if frame lt 1200 goto loop ------------------------------------------------------------------------------ 19) The ANALysis command Analysis module for computing solvent averaged properties It is accessed from the coordinate manipulation part (CORMAN) of CHARMM and is used with the following syntax. This piece of documentation is still under development. CLBIII 1/1/1990 NOTE: Keyword syntax changed after c25a2!! Unit numbers for output to file have to be specified, and the trajectory is now specified in the usual way with BEGIN,SKIP,STOP LNI 11/11/96 Keywords: (SOLVent: specifies analysis is to be of pure solvent, which means xref, yref and zref, or site keywords are inappropriate, i.e., analysis all configurations of solvent using all solvent molecules. OBSOLETE) WATEr: specifies the solvent is water (acutally any three-site molecule), and forces all distinct g(r)'s to be computed, i.e., g_oo, g_oh and g_hh. The first atom selection specifies the solvent atoms/molecules to be analyzed. (SPECies: specifies the solvent species. If SOLVent is active then all solvent molecules to be analyzed should be specified here, e.g., all of them present in the simulations. This keyword is followed by the standard selection syntax and is terminated with the FINIsh_solvent_specification keyword. OBSOLETE) SITE: Specifies the collection of atoms around which you would like to compute solvent properties, e.g., if you would like to analyze the solvent distribution and velocity correlation function around the center of geometry of a trp residue this keyword would be followed by the selection syntax which selects that residue. XREF, YREF, ZREF: specifies that solvent analysis around a specific spatial position, (xref, yref, zref) is to be carried out. This is the same as the site keyword, as far as the analysis of solvent configurations it invokes, however, this site is static whereas the SITE keyword permits selection of a dynamically evolving site. The above dimensions ar taken from trajectory stored informtion for crystal runs (w/ charmm22 or later) CROSs: allows the selection of two subset of atoms for g(r) analysis (a&b: 'a' are the atoms specified by the first selection and 'b' are the atoms specified by the second selection). The g(r) for a-vs-b and b-vs-b are calculated and returned in units IOH and IHH respectively. g(r) for a-vs-a will be returned in unit IGDIst. Note that CROSs does not exclude form the analysis the couple of atoms belonging to the same segid since it is design for the analysis of independent subset of solvent molecules. NOTE: The keyword CROSs cannot be selected with the following options: WATer, SITE, IKIRkg, ISDIst, IFDBf. IVAC, IMSD, IFMIn were not tested with CROSs. IVAC cannot be combined with any analysis requiring coordinates IGDIST and ISDIST are mutually exclusive flags NCORs = number of steps to compute vac or msd RSPIn = inner radius for vac,msd, analysis around REF (or SITE) RSPOu = outer radius for vac,msd, analysis around REF (or SITE) RDSP = radius of dynamics sphere, used for densities, kirkwood and dbf DENS = density (atoms/A**3) to use in normalization of g(r) if the value as calculated from the density within RDSP is not satisfactory DR = grid spacing for analysis of rdf's RSPHere = radius around REF to use for rdf analysis MGN = number of points in g(r) curve RCUT = radius of interaction sphere in dbf calculation ZP0 = initial reference site - dynamics sphere origin separation NZP = number of separations to compute dbf TYP = for DBF calc 1=oxygen, 1=hydrogen IHIS = unit for output of 3Dhistogram data (in "DN6" format) or IPDB = unit for output of "atoms" where density exceeds THREshold with options: WEIG use WMAIN to weight points !! Not tested DIPO accumulate dipole vector density !! NOT working yet (June 98) CHARge accumulate charge density !! Not tested default is to just accumulated number density of sel. atoms NORM value densities are divided by this value (and by number of frames) (default 1) XMIN,XMAX,DX YMIN,YMAX,DY grid dimension&spacing (default +/- 20A,0.5A spacing) ZMIN,ZMAX,DZ THREshold value for density to output atoms in PDB file format The atoms indicated by the solvent selection are analyzed. If dipole data is to be analyzed the selection should contain 1 atom/group - the groups define what atoms are to be used for the dipole calculation. This could be automated; also need minimum image combined with orienting function. IDIP specifies a unit to which a simple dipole distribution will be plotted. This facility is intended for use with polarisable modelling of bulk solvent, and requires the FLUCQ compilation keyword for activation. (If IDIP is not specified, then no distribution is plotted.) MINDipole real The minimum dipole (in Debye) to plot (default 0) MAXDipole real The maximum dipole to plot (default 4.0 Debye) NUMDipole int The number of sampling points to use (default 100) EXVC EXcludedVolumeCorrection for use with ISDIST - the soulte-solvent g(r) is corrected for the volume excluded around the solute (ie the SITE) by the atoms in the selection following EXCV. This correction is computed using a Monte Carlo procedure with parameters: MCP int Total number of points to use in the Monte Carlo (default 1000) MCSHells int Total number of equal volume shells to spread the MCP in (10) RPRObe real Probe radius (1.5A); a point is considered as excluded if it is within RPRObe+VDWR(i) of any atom i in the EXVC set ISEEd int Seed for random number generator (3141593) WEIG Use WMAIN instead of the vdW radii The following has been found to give good results even when looking at g(r) for water hydrogens around a site: scalar wmain = radius scalar wmain mult 0.85 coor anal ...... EXVC select segid pept end - MCPoints 20000 MCSHells 20 WEIG RPRObe 0.0 The key is to make sure that the a non-zero accessible volume is obtained at the shortest distances where g(r) starts being non-zero. The data file produced with EXCV contains two extra columns; column 4 contains the uncorrected g(r) and column 5 contains the accessible volume fraction. EXAMPLES: (See also the test/c27test/solanal2.inp testcase) The following examples use a trajectory of a short peptide in a periodic water box ! MeanSquareDisplacement of all watermolecules to estimate diffusion coeff open unit 21 read unform name @9pept500.cor open unit 31 write form name @9pept500.msd coor anal select type oh2 end - ! what atoms to look at firstu 21 nunit 1 skip 10 - ! trajectory specification imsd 31 - ! flag to do the MSD analysis rspin 0.0 rspout 999.9 - ! we are interested in ALL waters ncors 20 - ! compute MSD to NCORS*SKIP (0.04ps)steps xbox @6 ybox @7 zbox @8 ! and we did use PBC ! g(r) for the waters; the program defaults are used to calculate the density ! using selected atoms within 10A (RDSP keyword) of the reference point (0,0,0) ! (REF keyword) open unit 21 read unform name @9pept500.cor open unit 31 write form name @9pept500.goo open unit 32 write form name @9pept500.goh open unit 33 write form name @9pept500.ghh ! specify WATEr to get all three g(r) functions computed coor anal water select type OH2 end - firstu 21 nunit 1 skip 10 - ! trajectory specification igdist 31 ioh 32 ihh 33 - ! flag to do the solvent-solvent g(r) mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR rsph 999.9 - ! use ALL waters for rdf calculation xbox @6 ybox @7 zbox @8 ! and we did use PBC ! g(r) backbone amide hydrogen - water oxygens ! if a single solute atom is looked at the MULTi keyword is not necessary ! when several solute atoms are specified as the site, their average position ! will be used as the reference position if MULTi is not present open unit 21 read unform name @9pept500.cor open unit 31 write form name @9pept500.gonh coor anal select type oh2 end - ! Water oxygens site select type H end multi - ! and the amide hydrogens firstu 21 nunit 1 skip 10 - ! trajectory specification isdist 31 - ! do the g(r) (here solute-solvent) mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR rsph 999.9 - ! we use ALL waters for the calculation xbox @6 ybox @7 zbox @8 ! and we did use PBC ! g(r) for GLY3 NH - the water oxygens - with excluded volume correction open unit 21 read unform name @9pept500.cor open unit 31 write form name @9pept500.gn3ox1 coor anal select type OH2 end - site multi select atom pept 3 H end - EXVC select segid pept end - MCPoints 2000 MCSHells 20 RPRObe 1.7 - firstu 21 nunit 1 skip 50 - ! trajectory specification isdist 31 - ! flag to do the solvent-solvent g(r) mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR rsph 999.9 - ! we use ALL waters for the calculation xbox @6 ybox @7 zbox @8 ! and we did use PBC - Subcommand RCOR (Rotational Correlation Time of Water) Calculation of rotational correlation times corresponding to the three rotational motions of a water molecule has been added to the solvent analysis code. The three rotational motions refer to motion around the dipole axis (twist), around an axis perpendicular to the molecular plane (rock) and around an axis parallel to the H-H vector (wag) (Ref 1). The correlation time is calculated by fitting the exponentional decay part of the corresponding time correlation function C(t) to an exponentional function of the form C(t) = A exp(-t/tau) where tau is the correlation time. The direct correlation functions were calculated via FFT method using the CORFUNC subroutine in the CORREL.SRC. The calculation can be invoked by assigning a non-zero integeer value to the keyword RCOR. Keywords for rotational correlational time calculation are: RCOR <integer> - if RCOR > 0, invokes rotational correlational time analysis ROUT <unit> - write the three correlation functions of selected waters into a fortran unit TLOW <real> - lower limit of time for fitting, default is 1.0ps TUP <real> - upper limit of time for fitting, default is 4.0ps (Ref 2) MAXT <integer> - maximum number of time steps, default is 512 P1 - compute P1 dipole correlation instead of wag/twist/rock (< u(t)u(t+tau)>, where u is unit vector along water dipole output is to unit specified by ROUT P2 - compute P2 dipole correlation instead of wag/twist/rock (<P2( u(t)u(t+tau) )>, where u is unit vector along water dipole; P2(x)=(3x**2-1)/2 output is to unit specified by ROUT For P1 and P2 the analysis may be performed in a shell defined by RSPIn and RSPOut, and the minimum image xbox,ybox,zbox is also accounted for REFERENCE: 1. Johannesson, H. and Halle, B. J. Am. Chem. Soc. 1998, 120, 6859-6870 2. Wallqvist, A. and Berne, B. J. J. Phys. Chem. 1993, 97, 13841-13851 EXAMPLE: see test/c27test/solanal2.inp ! Rotational Correlation Time of Water open unit 21 read unform name @9pept500.cor open unit 31 write form name @9pept500.rcor coor anal sele .byres. (type oh2 - ! select all three atoms of water .and. (resn asp .and. type od1) - .around. 3.5) show end - firstu 21 nunit 1 skip 10 - rcor 1 - ! rot corr time calculation timl 1.0 timu 3.0 - ! lower and upper time limits for linear fit rout 31 - ! corr coef to unit 31 xbox @6 ybox @7 zbox @8 ! and we did use PBC - Subcommand IHYD: Hydration Number Calculation This is to calculate hydration number or, in general, the number of solvent molecules within a specified distance of a multi atom or single atom site: * number of solvent molecules (residues) withn RHYD of the solute * number of solvent atoms within RHYD of the solute * number of solvent atoms within RHYD of solute atoms (ie, if three water molecules are all within RHYD of a 7-atom solute this will be 63) Sets CHARMM variables NHYDRR, NHYDAR and NHYDAA to the averages for these three numbers. If IHYDN>0 these numbers are written to unit IHYD every timestep. At the end averages over the trajectory are printed in the output file. Hydration number calculation is invoked by specifying a non-zero cutoff RHYD. NB! You need keyword MULTi if the solute (the SITE) has more than one atom. Keywords for hydration number calculation are: IHYD <integer> - if IHYDN > 0, output to unit IHYDN each timestep RHYD <real> - calculate hydration number at this distance from each atom in the site Example: ! Calculate hydration no coor anal sele resn tip3 .and. type oh2 end - site select resn asp .and. type od1 show end multi - firstu 21 nunit 1 skip 5 - rhyd 3.0 - ! calculate hyd no at 3.0A xbox @6 ybox @7 zbox @8 ------------------------------------------------------------------------------ 20) The DRAW command The DRAW command (called directly from CORMAN, not to be confused with the DRAW command found under the ANALysis command) is useful for displaying molecules. The output is a command file that can be read by various displaying and plotting programs. This command file can be edited for different types of displaying. In addition to atom positions and bonds, velocity and forces may also be displayed. The current keywords are: NOMO - No molecule option (only velocities or derivatives) DFACt - Derivative factor (default 0.0) DASH - Spacing of dashed line used for Hbonds (default .01) FRAMe - Specifies that a frame tag will be written first (default - dont specify frame) RETUrn- Specifies which stream the plotting program will return to after plotting this section (default none) An atom selection is also looked for. Any atom not selected will not be considered. The default is to include all atoms. ------------------------------------------------------------------------------ 21) The HBONd command The CONTact command The HBONd command analyses a trajectory, or the current coordinates, for hydrogen bonding patterns. The form COOR CONTact ... ignores the hydrogen bond donor/acceptor definitions in the psf and looks for all contacts which satisfy the distance cutoff criterion between all atoms in the two selections; possibly bridged by a residue as defined by the BRIDge keyword. This is useful for hydrophobic contact analysis, or for salt bridges. No angle cutoff can be used with this form of the command. Output and other options are as for the COOR HBONd variant. The form COOR HBONd makes use of the DONOR/ACCEPTOR definitions in the psf. For each acceptor/donor in the first selection the average number and average lifetime (for trajectories only) of hydrogen bonds to any atom in the second selection is calculated. A hydrogen bond is assumed to exist when two candidate atoms are closer than the value specified by CUT (default 2.4A, (reasonable criterion, DeLoof et al (1992) JACS 114,4028), and if a value for CUTAngle is given the angle formed by D-H..A is greater than this CUTAngle (in degrees, 180 is a linear H-bond); the default is to allow all angles. Keyword VDWR specifies that the cutoff for each case will be set to CUTOFF = VDWR(ACCEPTOR) + VDWR(DONOR_HEAVY_ATOM) + CUT This is useful when atoms of very different size (eg S.H.O and N.H.O) can be involved in the hydrogen bond, such that a single cutoff value is inadequate. The default for CUT in this case is -1.1A (note that it is a negative number). The current implementation assumes that hbonding hydrogens are present in the PSF and uses ACCEptor and DONOr information from the PSF to determine what pairs are possible. If output is wanted to a separate file the IUNIt option can be used. If the BRIDge option is used the routine calculates average number and lifetime of bridges formed between all pairs of atoms in the two selections; a bridge is counted when a residue of the type specified with the BRIDge <resnam> hydrogen bonds (using same criteria as for direct hbonding) to at least one atom in each selection. The typical use of this would be to find water bridges. Here again, results are presented for each atom in the first selection. If FIRSTunit is not specified the current (MAIN) coordinates are analyzed. Periodic boundary conditions are taken into account using the hardwired minimum image code (see bound ) if keyword PBC is given. Supported geometries are: Geometry Keyword Required information Auxiliary information "Orthogonal" CUBIC BOXL (or XSIZE) YSIZE, ZSIZE if different from XSIZE Truncated octahedron TO BOXL (crystal A parameter) Rhombic dodecahedron RHDO BOXL (crystal A parameter) If crystal information is present in the trajectory it will be used to set the actual box dimensions (overriding the value(s) specified on the COOR command line). The minimum image code is turned off when the command exits, which means that a previous BOUND command will no longer be in effect. Keyword VERBose provides a more detailed output: For trajectory analysis the duration and endtime (ps) of each H-bond, or bridge, together with a specification of the atoms involved is output; potentially very large amounts of data! Only hbonds/bridges with a lifetime longer than the value specified by keyword TCUT (default 0.0 ps) are included here and in the summary. NB: TCUT (and NSKIP) may influence the results, since hbonds with a duration < TCUT are not counted, and for the lifetime analysis a quick fluctuation in hbond distance may with one choice of NSKIP result in the hbond being perceived as broken at that instant, whereas with a longer NSKIP the event would not have been noticed, resulting in a longer lifetime being reported. For single coordinate set analysis the VERBose keyword results in a more detailed listing giving all atoms involved, and also the geometry for direct hbonds. For each donor/acceptor in the first selection the trajectory analysis outputs the AVERAGE NO. of hydrogens bonds this atom has had during the trajectory (aveno=sum over frames(number of hbonds formed by this atom)/(number of frames) the average lifetime is defined as avelife= sum over hbonding events(duration of hbond between two atoms)/(number of different hbonds formed by these atoms) (ie, hbonds that have been broken for at least one frame between events) Note that the lifetime can be influenced by end-effects (ie hbonds still active at end of trajctory are counted as being terminated then!) Output can be directed to a separate file specified by IUNIT int. If the VERBOse option is on, the atoms actually involved in a hydrogen bond are flagged in two selection sets named HBDEFI and HBDEFJ for atoms in the first and second selections, respectively. For COOR HBOND BRIDG the first atom in each bridge residue actually involved in a bridge is flagged in a set named HBDEFB. Note that this is NOT the same as all donors/acceptors in the selections. This should work for trajectories (not tested) but it is probably most useful when applied to a single coordinate set (possibly inside a CHARMM loop). Examples: 1/ Find the atoms that are hydrogen bonded COOR HBOND SELE SEGI A END SELE SEGI B END VERBOSE DEFINE ASET SELE HBDEFI END ECHO Number of atoms in segi A that are involved in hydrogen bonds: ?NSEL ------------ 2/ Find bridging waters (W) that are hydrogen bonded to segment A and segment B through another water molecule: A..wA..W..wB..B COOR HBOND SELE SEGI A END SELE RESN TIP3 END VERBOSE DEFINE WA SELE HBDEFJ END ! water molecules wA COOR HBOND SELE SEGI B END SELE RESN TIP3 END VERBOSE DEFINE WB SELE HBDEFJ END ! water molecules wB COOR HBOND BRIDGE TIP3 SELE WA END SELE WB END VERBOSE The following charmm substitution parameters are set in the module: ?NHBOND = total number of hydrogen bonds for selected atoms (timeaveraged) ?AVNOHB = average number of hydrogen bonds over selected atoms (timeaver.) ?AVHBLF = average lifetime of hydrogen bonds Note that these averages are over the selected atoms, which may include a number of atoms with no hbonds > TCUT! Distance and lifetime histograms can be computed for all (putative) hydrogen bonds encountered in the analysis; ie, the distance histogram will in general contain non-zero data also for bins > CUT. For bridges the lifetimes are those of the bridging events, but the distances are computed from all individual hydrogen bonds. The three columns in the output are: distance (or time) counts counts/NSTEP where NSTEP is the number of frames that have been analyzed from the trajectory. Keyword default meaning IRHI -1 unit to which distance histogram will be written DRH 0.05 bin size for distance histogram (A) RHMAx 10.0 distance in maximum bin (collects all distances >= RHMAx) ITHI -1 unit to which lifetime histogram will be written DTH 5.0 bin size for lifetime histogram (ps) THMAx 1000.0 time in maximum bin (collects all times >= THMAx) ------------------------------------------------------------------------------ 22) The HISTogram command This command computes a histogram along the X,Y,Z or Radial directions for the selected atoms. The histogram can either be a simple count of the number of atoms contained in each bin (specified by the HNUM=number of bins between HMIN,HMAX keywords), or if the WEIGhting keyword is present the WMAIN array is summed for the atoms in each bin. HSAVe specifies that the histogram should be saved and incremented at the next invocation of COOR HIST. HPRInt specifies that the resulting histogram should be printed. For X,Y,Z histograms the output is the accumulated density/HNORM (default=1.0) in each bin. If HDENS>0.0 (default=0.0) there is also a third column for R histograms containing the accumulated density/(volume of shell containing this bin)/DENS. The COMParison keyword results in XCOMP,YCOMP,ZCOMP,WCOMP being used. The variable ?NCONFIG is set to the number of configurations (frames) that have been accumulated so far. The results may be output to a file specified by IUNIt int. EXAMPLE: To average the charge density in spherical shells from a trajectory could be done in the following way: scalar wmain=charge traj iread .... set i 1 label loop traj read !if you are reading velocities, you may want to convert to A/ps ! (and then you wouldn't use the weighting option like this) ! scalar x divi ?TIMFAC ! scalar y divi ?TIMFAC ! scalar z divi ?TIMFAC coor hist R hnum 50 hmin 0.0 hmax 10.0 hsave weig incre i by 1 if i .lt. 100 goto loop ! you could also normalize for number of selected atoms ! set scale ?NSEL ! mult scale by ?NCONFIG ! then use @scale instead of ?NCONFIG below bomblevel -1 ! to get by the zero atom selected warning below coor hist R hnum 50 hmin 0.0 hmax 10.0 select none end hprint - hnorm ?NCONFIG [ hdens 0.03 (some reasonable bulk density/A**3) ] ------------------------------------------------------------------------------ 23) The PUCKer command COORdinates PUCKer [SEGId segid] RESId resid1 [TO resid2] [AS | CP] The sugar pucker phase and amplitude, as defined by Altona&Sundaralingam (default, keyword AS) or (CP) Cremer&Pople (JACS 1975), are calculated for the (deoxy)ribose of the specified residue(s); the first segment is the default. A range of residues from resid1 TO resid2 can be analyzed. ------------------------------------------------------------------------------ 24) The INERtia command COORdinates INERtia [atom-selection] Principal moments of inertia I_xx, I_yy, I_zz are calculated and the eigenvectors of the inertia tensor are printed. Normally atom selection should not be used and the command example: COOR INER is sufficient, since all ithe atoms are selected by default. The units for principal moments of inertia are amu * A^2, where amu - atomic mass unit (Carbon is 12), and A stands for Angstrom. ------------------------------------------------------------------------------ 25) The INERtia ENTRopy command COORdinates INERtia [atom-selection] ENTRopy [TEMPerature <real>] [SIGMa <real>] - [STANdard <SOLUtion|GAS>] Entropy calculation is an extension to the INERtia command. In addition to calculation of principal moments of inertia the rotational and translational entropy components will be evaluated. Calculation of these two entropy terms is very fast. See vibran.doc to see how to calculate the vibrational entropy term. Default value for TEMPerature is 298.15 K. Default SIGMa value is 1.0. SIGMa is symmetry number which is 1 for non-symmetric molecule and some low symmetry groups. For symmetric molecules one should enter a correct value for sigma (see, for example, C.J.Cramer, "Essentials of Comp.Chem.", 2002,p.327). Translational component of entropy depends on the defition of standard state. There are two definitions: solution (1M) and ideal gas. The default is solution. They differ by a constant of 6.35236 kcal/mol, with higher entropy in gas state. See details inTidor and Karplus, J Mol Biol (1994) vol. 238 (3) pp. 405-14 example: COOR INER ENTRopy COOR INER ENTRopy TEMPerature 298.15 SIGMa 1 COOR INER ENTRopy TEMPerature 298.15 SIGMa 1 STANdard SOLUtion COOR INER ENTRopy TEMPerature 298.15 SIGMa 1 STANdard GAS VIBRan DIAGonalize ENTRopy TEMP 298.15 SIGM 1 DIAGonalize ENTRopy TEMP 298.15 SIGM 1 STANdard SOLUtion DIAGonalize ENTRopy TEMP 298.15 SIGM 1 STANdard GAS END testcase in c32test/entropy.inp The units for entropy are cal/(mol*K). Rotational, translational, vibrational, and total entropies can be accessed in CHARMM input file as ?SROT, ?STRA ?SVIB, and ?SSUM substitution parameters. 26) The SECondaryStructure command (SECS) Computes secondary structure of residues in first-selection in the context of the second-selection; eg, a beta-strand in the first-selection will be rcognized as such if it forms appropriate hydrogen bonds to residues in the second-selection. If no second-selection is given it is the same as the first (which defaults to all). A residue is included if any atom in it is selected, and amino acids are recognized by the presence of atoms named N,C and CA. The amide hydrogen can be named either H or HN. Only operates on main coordinates. Currently using Kabsch&Sander (Biopolymers 22, 1983, 2577) definition of alpha-helix and beta-strand. Sets CHARMM variables ?NALPHA and ?NBETA to number of residues in alpha/beta structures, and ?ALPHA and ?BETA are set to fraction of residues with that type of structure. The fraction is computed from number of peptide residues in the first selection. On return Calphas have WMAIN-array set to 0, 1 (alpha), 2 (beta) The default H-bond criterion is CUTH=2.6, slightly longer than the default 2.4A used in coor hbond (from DeLoof et al JACS 1992); this is to be slightly more generous in defining secondary structures. CUTA can be used to define an angle cutoff for the N-H..O angle (default is not to use this criterion). Keywords QUIEt/VERBose control the amount of output In the calculation of % alpha the end residues of the helix are included, which deviates from the K&S definition. Keyword STRIct enforces adherence to K&S. ----------------------------------------------------------------------------- 27) The CONFormational command COORdinate CONFormational { <resname> } [ PRINT ] [ READ io-speficication ] - [atom-selection] [COMP] Current methods for generating transition paths between macromolecules e.g., the TMD and TREK modules, rely on the Cartesian coordinates of a subset of atoms in a protein. Although several residue types possess symmetry (e.g. planar symmetry of a PHE ring), so that the conformation of such a residue is invariant with respect to a rotation around the symmetry axis, rendering certain groups of atoms effectively indistinguishable, topology files must distinguish between these atoms (e.g. PHE CD1 vs. PHE CD2). Given two different coordinate sets for a macromolecule, any two-set path generation method that makes use of the Cartesian coordinates of atoms that belong to residues with symmetry decides arbitrarily the correspondence between the `indistinguishable' atoms. For example, performing TMD using coordinates of the ring atoms of a PHE, will force the position of atom CD1 in the initial set to move to the position of atom CD1 in the target set, although the movement from CD1 to CD2 is also possible. In such transitions, it is likely that there exist a path with a high energy barrier (e.g. flipping of a PHE ring in a tightly-packed protein interior) that can be avoided by making use of symmetry. The current method, CONFormational consistency, is an algorithm for renaming certain atoms to minimize rotation and flipping of the involved residues during path generation. The algorithm is heuristic and is as follows. (Two coordinate sets are assumed present, in the main and comparison sets). For each residue in the optional atom selection, the following procedure is performed. The residue is partitioned into three (non-disjoint) sets of atoms: swap atoms, orientation atoms and test atoms. Swap atoms are organized into pairs, which will be swapped during the check. The residues in the two conformations are RMSD- aligned based on the orientation atoms only. RMSD is computed between the test atom positions in the two coordinate sets. The configuration of the swap atoms that gives the lesser test-atom-RMSD value is accepted. Positions of any hydrogen atoms that are bonded to swap atoms are initialized, and can be regenerated with HBUIld. The three sets in the residue partitioning are defined by default for the following residues (i.e. by default, {<resname>} can contain any number of these) ARG ASP GLU HIS HSC HSD HSE HSP LEU PHE TYR VAL Users can override pre-existing defaults for these residues, and declare new residues in an optional input file. In the following, the default residue partitioning is shown for ARGinine (only the relevant atoms are shown): HH11 | -- CD NH1-HH12 \ //(+) NE--CZ \ NH2-HH22 | HH21 swap atoms: NH1 NH2 orientation atoms: CZ NH1 NH2 test atoms: CD Note that the HH* hydrogens will have undefined positions after the check is complete, and can be redefined using HBUIld. Also note that more than one partitioning scheme may lead to the same results. A custom residue partitioning file can be specified, following the READ option. For the twelve residue types supported by default, the equivalent partitioning file is: 12 ARG 1 CD 1 CZ 1 NH1 NH2 0 ASP 1 CA 2 CB CG 1 OD1 OD2 0 GLU 1 CB 2 CG CD 1 OE1 OE2 0 HIS 1 CA 2 CB CG 2 ND1 CD2 NE2 CE1 0 HSC 1 CA 2 CB CG 2 ND1 CD2 NE2 CE1 0 HSD 1 CA 2 CB CG 2 ND1 CD2 NE2 CE1 0 HSE 1 CA 2 CB CG 2 ND1 CD2 NE2 CE1 0 HSP 1 CA 2 CB CG 2 ND1 CD2 NE2 CE1 0 LEU 1 CB 1 CG 1 CD1 CD2 0 PHE 1 CA 3 CB CG CZ 2 CD1 CD2 CE2 CE1 0 TYR 1 CA 3 CB CG CZ 2 CD1 CD2 CE2 CE1 0 VAL 1 CA 1 CB 1 CG1 CG2 0 The first line specifies the number of lines to be read (number of residues) Each subsequent line is organized as follows: <residue name> <# test atoms> <list of test atoms> - <# orientation atoms that are not swapped> <list ...> - <# PAIRS of orientation atoms that are swapped> <list...> - <# swap atoms that are not part of the orientation set> <list...> Note that the default residue partitioning file includes residues which do not have any symmetry. These are histidine residues : HIS, HSD, HSE, HSP, and HSC. In these cases the atoms ND1 and CD2 are assumed to be indistinguishable. The optional PRINT command will print checking information for each tested residue By default, the main comparison set is modified. Specifying COMP will cause the comparison set to be modified (note that this may lead to undefined hydrogen atoms in the comparison set). Finally, an atom selection may be specified. In this case, only the residues for which at least one atom is selected will be tested. Examples: 1) coor conf his arg phe tyr hsd glu asp print select all end will check the specified residues and, if needed, make modifications to the main set. Results for each residue will be printed. Default partitioning is used. 2) coor conf arg print select all end read * residue partitioning file ARG 1 CD 1 CZ 1 NH1 NH2 0 ASP 1 CA 2 CB CG 1 OD1 OD2 0 will check all arginines using the custom partitioning specified below the command line Testcase: c35test/confcons.inp ----------------------------------------------------------------------------- 28) The PATH command COORdinate PATH { NREP <int> } {NAME <character*>} [<PDB|FILE|UNFO|CARD|FORM>] This command will create an interpolated path connecting two structures stored in the main and comparison sets. Currently, only linear interpolation in Cartesian atom coordinates is implemented. NREP specifies the number of replicas desired (this includes the two endpoints, and must be at least three) NAME specifies the base name of the file to which the interpolated coordinates will be written. An extension will be appended to the base name, which consists of a number in the range [0.. NREP-1] followed by '.<ext>', in which ext depends on the format specification as follows: format spec ext -------------------- PDB PDB FILE/UNFO/CARD COR Example: coor path nrep 32 name output/conv card ! will create a linearly interpolated path of 32 replicas named ! output/conv0.cor, ..., output/conv31.cor ! in card format Testcase: c35test/confcons.inp ----------------------------------------------------------------------------- 28) The DRMS command COORdinate DRMS [2x] (atom-selection) Computes the Distance RMS - the RMS of differences in interactomic distances between the main and comparison sets. This is a translation/rotation invariant measure of structural similary and needs no strucural alignment. For all distances Rij between one atom i in the first selection and one atom j in the second selection the difference Dij=(Rij(main) - Rij(comp))**2 is computed, and DRMS= SQRT(SUM(Dij)/NBPAIR), where the sum is over the NBPAIR total number of interatomic distances included in the calculation. Both atom i and atom j must have defined coordinates. No selection means all atoms are used. If only one selection is given, all atom pairs within the selection are used, except that if i and j refer to the same atom this pair is not included. There is no check for bonded connectivity. Examples: COOR DRMS SELE TYPE CA END COOR DRMS SELE TYPE CA .AND. HELIXONE END SELE TYPE CA .AND. HELIXTWO END DRMS is set to -1.0. Testcase: c40test/drms.inp ----------------------------------------------------------------------------- 29) The SMAP command Reference: K. M. Ravikumar and W. Hwang, JACS 133:11766 (2011). This command calculates the solvation map by analyzing coordinate trajectories. A region of interest (e.g., around a group or protein surface) is divided into a cubic grid of cells with size RESOlution (default=0.7A, half the radius of water) and water properties during a dynamics run are calculated for each cell. Available properties are: SDEN (water density), DIFT (translational diffusion coefficient), and HBONd (average number of hydrogen bonds that water molecules in the cell form). The command is parallelized and works with mpirun. Outputs are written to the following units (should be opened beforehand): For water density, IUNWrite (used with SDEN, DIFT, or HBOND), and for diffusion coefficient (DIFT), IDIF. For number of hydrogen bonds (HBOND), three units are used: ISLV (H-bonds with other water molecules), ISLT (H-bonds with solute atoms, including those not in the given atom selection; selection is used only to determine the grid box size and to align coordinate frames), and ITOT (H-bonds with both solute and solvent). The output format can be the MRC electron density map format (EMAP) or CARD. Since the output file can be large, only region within RCUT (default: 9999.9999 A) from selected atoms is used for calculation. To initially determine the search box where solvation map is calculated, the comparison coordinate set must be present. If the comparison set is absent, the main set must be present and it is copied to the comparison set. With the ORIE option, at each frame, selected atoms are aligned to those of the comparison set. This is for the case when solvation map relative to a moving domain is desired. Note that if the selected atoms change conformation too much (as for a flexible loop), the resulting solvation map may not be reliable. If NORO option of ORIE is present, alignment is done by translation only (no rotation), which yields a radially isotropic map relative to the selected atoms. NOTE: Behavior of atoms moving across a periodic box is not accounted for in the SMAP command. If the selected reference atoms (solute) are near the boundary of a periodic box or move across it, coordinate trajectory must be processed beforehand using the MERGE command, so that the reference atoms stay surrounded by water molecules and are away from the boundary by more than RCUT. Otherwise, low density will result due to the empty region outside the boundary. Or very high water diffusion coefficient may be reported as water moves across the boundary. The SOLVent option (default: OH2) is used to designate the solvent atom type used for calculation. For example, 'SOLV H1' uses the H1 atom of the water molecule for calculating the map. 'SOLV SOD' generates map for sodium ions. For water density (SDEN), the number of frames that each cell is visited by SOLV atoms is counted, and is divided by the cell volume. Water density is also calculated with HBOND or DIFT, but SDEN is faster. EXAMPLE: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! To get density around water residue 1 and write into an EMAP file: set R0 0.7 ! resolution of the map define ratom sele segi W0 .and. resi 1 end read coor dynr curr name XX.rst coor copy comp coor orie comp sele ratom end coor orie comp sele ratom .and. type OH2 end ! Put OH2 at the origin ! Since the origin is at the corner of a cell, translate water oxygen by half ! the cell size, which makes the EMAP density to be aligned to the center of ! the cell. This is for visualization purpose (e.g., in UCSF Chimera). calc r1 0.5*@{r0} coor trans comp xdir @{r1} ydir @{r1} zdir @{r1} sele ratom end ! In YY.dcd, ratom must be surrounded by water all the time. open read unit 10 file name YY.dcd open emap unit 11 file name ZZ.mrc coor smap sden reso @{r0} rcut 15 iunw 11 first 10 nunit 1 - orie sele segi WAT .and. resi 1 end emap !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! SMAP DIFT calculates translational diffusion coefficient. Between two successive coordinate frames, square of the displacement of the SOLV atom is calculated and is stored in the cell where the atom visited at the first of the two frames (in the second frame, the atom may have moved to another cell). After all frames are read, the mean square displacement for each cell, averaged by the number of times that the cell is visited, is divided by 6*dt (dt: coordinate saving time interval), to yield the translational diffusion coefficient for the cell. Calculation of solvent displacement between two frames is unaffected by the ORIE option, as the difference in coordinate translation/rotation for aligning the system to reference atoms between the two frames is accounted for. Additional options for DIFT: WDISt (default -1, disabled): When displacement of a solvent atom between two frames is greater than WDIST, issue level -1 warning. DCUT (default -1, disabled): Only consider cells with water density greater than DCUT for diffusion coefficient calculation. Set diffusion coefficient for other cells to zero. This is for considering only high-density regions. HCUT (default -1, disabled): When positive, only consider regions with diffusion coefficient lower than HCUT, and set diffusion coefficient for other regions to zero. This is for considering water near surfaces whose diffusion coefficient is lower than that for the bulk water, or to region near the boundary of the simulation box that has high diffusion coefficient due to water molecules moving across the periodic box. EXAMPLE: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Calculate translational diffusion coefficient relative to ratom (defined ! beforehand) for cells with water density greater than 0.05/A^3 (1.5 times ! the bulk density), and translational diffusion coefficient lower than 6 ! A^2/ps. Write output in the MRC electron microscopy files. open emap unit 11 file name map_sden.mrc open emap unit 12 file name map_dift.mrc coor smap dift reso 0.7 rcut 15 iunw 11 idif 12 first @j nunit 1 - sele ratom end emap hcut 6 dcut 0.05 orie !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! SMAP HBONd calculates the average number of hydrogen bonds formed by the water molecule(s) in a cell. Since this applies even to a cell that is visited only once by a water molecule during the simulation, the option DCUT (default=-1.0; no cutoff) is used to consider only cells with water density higher than DCUT. The CUTHB (default=2.4 A) option is similar to that for the COOR HBOND command. NOTE: If RESO (linear size of a cell) is very large, more than one water molecule can be counted within a cell. While this does not affect the density calculation (since the cell volume is correspondingly large), the number of H-bonds is the total for all the water molecules visiting the cell. SMAP HBONd command uses the donor/acceptor atoms defined in the residue topology file. To include atoms that are not defined as donor or acceptor (e.g., ions), they need to be added using the DONO/ACCE ADD command. EXAMPLE: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! calculate number of hydrogen bonds relative to ratom (defined beforehand) ! for cells with water density greater than 0.05/A^3 (1.5 times the bulk ! density), and write in the MRC electron microscopy files. open emap unit 11 file name hb_tot.mrc open emap unit 12 file name hb_slv.mrc open emap unit 13 file name hb_slt.mrc coor smap hbond reso 0.7 rcut 15 itot 11 islv 12 islt 13 first 10 nunit 1 - sele ratom end emap orie dcut 0.05 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Top Coordinate Manipulation Values There are several different variables that can be used in titles or Here is a summary and description of each variable. See also subst.doc (which may be more up-to-date). ---------------------------------------------------------------------------- 'XAXI','YAXI','ZAXI','RAXI','XCEN','YCEN','ZCEN' A rotation axis vector and its length and the center of rotation. This data is set by the COOR AXIS, COOR LSQP, COOR ORIE, and COOR ORIE RMS commands. These values may be used by any of the commands that uses the vector-spec with the AXIS keyword. ---------------------------------------------------------------------------- 'XMIN','YMIN','ZMIN','WMIN','XMAX','YMAX', 'ZMAX','WMAX','XAVE','YAVE','ZAVE','WAVE' Statistics set by the COOR STAT command. ---------------------------------------------------------------------------- 'THET' Angle of rotation set by the COOR ORIEnt command. ---------------------------------------------------------------------------- 'XMOV','YMOV','ZMOV' Displacement of centers set by the COOR ORIEnt command. ---------------------------------------------------------------------------- 'RMS' Resulting RMS value set by the COOR RMS, COOR ORIEnt, or COOR RGYR commands. ----------------------------------------------------------------------------- 29) The TMSCore command Computes the TM-score between the selected sets of atoms. The TM-score (see Zhang, Y. and Skolnick, J. Proteins, 2004 57:702-710) is a scoring function that quantifies the similarity between two structures, returning a number between 0 and 1. We assume that the sequences of the two structures are identical. The TM-score is computed as: TM-score = Max [ 1/N sum_{i=1}^N 1/(1 + (di/d0)**2) ] where di is the distance between the two structures of atom i, d0 is a constant reference length that depends only on the number of residues in the protein, N is the number of atoms selected, and the Max is computed over many different alignment attempts of the two molecules (see Zhang and Skolnick for more details). The aim of the multiple alignments is to emphasize the matching parts of the molecule. After the command is executed, the TMScore, the TMScore with a cutoff of 10 A, and the d0 value used to compute the TMScore are assigned to the variables ?tmscore, ?tm10 and ?tmd0, respectively. Ex/ coor tmsc sele type CA end