Input-Output Commands The commands described here are used for reading and writing data structures used in the main part of CHARMM. Some of data structures used in the analysis facility may also be read and written. * Read / Reading data from external sources * Write / Writing data structures in machine readable form * Print / Writing data structures in a human readable form on unit 6 * Titles / Specifying and manipulating titles * IOFORM / Specify PSF file format
Top READ - Reads Data from External Sources This command reads data into the data structures from external sources. The external sources can be either card image files or binary files. The fortran unit number from which the information is read, is specified with the unit-spec. The precise format of all these files is described only in the source code as that serves as the only definitive, accurate, and up to date description of these formats. The description of the data structures provides pointers to the subroutines which should be consulted, see *note data: (usage.doc)Data Structures. * Read Syntax / Syntax of the READ command * Segments / Reading segments'sequences and coordinates * Sequence / Reading a segment's sequence * Coordinate / Reading coordinates * Universal / Reading coordinates from nonstandard formats * Param Files / The formats used in parameter files * RTF File format / The format used in topology files * Other files / Reading all other file types
Top Syntax of READ Command [SYNTAX READ] READ { RTF { CARD [APPEnd] [PRINt] } } [ UNIT integer | NAME filename ] { { [ FILE ] } } { PARAmeter { CARD [PRINt] [APPEnd] [FLEX] } } { { [FILE] [NBON ] [MMFF] } } { IC { [ CARD ] } [ APPEnd ] [ SAVEd ] } { { FILE } } { SEQUence { [ CARD ] } } { { COOR [ RESId ] [SEGI <segid>] } } { { PDB [ RESId ] [CHAIn <char>] } } [SEGI <segid>] } } [NCHAin <int] } } [repeat(SKIP <resn>)] } } [repeat(ALIAs <resold> <resnew>)] } } [SEQRes] } } [FIRStresid <int>] } } [HETAtm] } } [NOATom] } } { { TIPS integer } } ! TIP3P water model { { ST2 integer } } ! ST2 water model { { WATEr integer } } ! OH2 residue model { { DUM integer } } ! Dummy atoms { { resname integer } } ! Any RESI in the RTF { HBONd { [ FILE ] } } { { CARD } } { PSF { [ CARD ] [ XPLOR/OLDPSF ] } [APPEend] } { CONStraint { [ CARD ] } } { NBONd [ FILE ] } { TABLe [ FILE ] } { BTABle [ FILE ] } { TRAJectory [ COMP ] } { IMAGes [ CARD ] [ INIT ] } { XRAY } { UNIVersal-coordinate-format } { COORdinate coor-spec [ COMP ] } { SEGId segment { PDB } [BUILd [SETUp]] } { { CARD } } { { FREE } } { NAMD FILE "filename" ** } ** no other options are available {NM } coor-spec ::= { FILE [IFILE int [CONTinue]] } coor-option { CARD [OFFS int] [ RESI ] } { PDB [OFFS int] [MODEL int] [OFFI] } { UNIVersal [OFFS int] [ RESI ] } { IGNOre } { DYNR CURR|DELT|VEL } { TARG } { TAR2 } coor-option ::= [APPEnd] [INITial] [FREEfield] atom-selection Syntactic ordering: The second field must be specified as shown. The file to be read can be specified either through the UNIT number (the same number as in a preceding OPEN statement) or through the NAME keyword. Options exist to read/write the PSF in two alternative formats, the "standard" writing of PSFs use the XPLOR format (which replaces the atom type code for for each atom (IAC(I)) with the character string for the atom type from the current RTF/PARAMETER pair (ATC(IAC(I)). This allows atom type code values to be generated at time of reading RTF or PARAMETERs, via use of a -1 in the "code" column of the MASS statement. Note: Caution should be use with some of the existing pert scripts as they reassign the atom type code using scalar commands and unless one is using a RTF/PARAMETER file with fixed atom types this will cause uncontrolled assignments of atom type codes, and corresponding parameters.
Top Reading the sequence and coordinates of segments simultanously This command provides convenient way to transform a system in PDB file format into new CHARMM segments with given coordinates. When read in segments from a PDB file, one can specify BUILd to generate all atom connectivities and atom types. If there are missing atoms in the PDB file, one can specify SETUp to generate an internal coordinate table of the segments to be used to generate the coordiantes of those missing atoms. Each chain in the PDB file will form a new segment named as the given SEGId followed by its segment number. These generated segments are well quialified CHARMM segments and can be used for atom based simulation. This is a very convenient way to generate simulation systems from PDB files. However, It requires that all residue and atom names in the input file are consistent with that in the For example: open read unit 10 card name 1b5s.pdb read segid b5s PDB build setup unit 10 This command can be used to create a new segment from either a PDB file (PDB), a CHARMM coordinate file (CARD), or a free format coordinate file (FREE). If BUILd option is not specified, the generated segment contains only atoms listed in the input PDB file but no atomic connectivities are generated. Such a segment can be used to generate a map object needed in the EMAP module (see emap.doc). With this command, a map object can be quickly converted from a PDB structure.
Top Specifying a sequence of residues for a segment The specification of SEQUence causes the program to accept a sequence of residue names to be used to generate the next segment in the molecule. Unless the WATEr, TIPS, or ST2 option is used, the sequence is specified as follows: title number of residues repeat(residue names) The form of the title is defined in the syntactic glossary, *note syn: (usage.doc)Syntactic Glossary. The number of residues is specified on the line following the title in free field format. If the number of residues you specify is less than zero, file. If the number is greater than zero, it will also stop once it has read at least as many residues as you've specified. If the number you specify is zero, you will get a warning message as one common error is to forget the number entirely. In this case, the first residue name will be consumed as the number and converted to zero. The residue names are specified as separate words, each no longer than 4 characters, on as many lines as are required for all the residues. This sequence may be placed immediately following the READ command if the unit number is the stream or may be placed in a separate file. When reading is complete, CHARMM will list all the residues it has read, and tell you which residues it thinks can be titrated. The WATEr option allows a sequence of water molecules to be specified. This will give the old 3-center water model (not recommended). The integer which follows the keyword gives the number of waters. The TIP3P water model may be specified with the TIPS option. Likewise, the ST2 option allows ST2 waters to be specified. Obviously, no sequence on separate lines need be given. The topology file must contain the residue named (OH2,TIP3,ST2); otherwise, the GENErate command invoked subsequently will fail. The COOR option will read the sequence from a CHARMM format card coordinate file. The residue numbers are ignored except that when a change occurs, a new residue is added. If the RESId keyword is also present, then the resid's are obtained from the resid field of the coordinate file. The SEGI <segid> option allows the sequence to be read only for the residues belonging to the corresponding segid in the coordinate file. For the PDB option resids are always read from the resSeq (resid) field. This is useful when one wants to specify residue names (rather than use the number representation). No other information is read from the coordinate file during this process. To read the sequence for a specific chain in a PDB file the CHAIn <char> option can be used; <char> is the one letter PDB chain id in position 22 of ATOM/HETATM records. If the SEGI <segid> option is used the sequence is read for the atoms that have the corresponding segid in columns 73-76 of the PDB file. NCHAin <int> starts reading from chain number <int> as defined by TER separator records. Variables SQNRES and SQRESID are set to the number of residues read and the SEGId used. By default only ATOM records are read. The HETAtm keyword allows HETATM records as well, and the NOATom keyword turns off reading of ATOM records. SKIP specifies residue names that will be ignored, and the ALIAs keyword provides a simple residue name translation facility: Each instance of <resold> will be replaced by <resnew>. With the keyword SEQRes the sequence will be read from SEQRES records, which is useful when there are missing residues in the ATOM records. Here FIRStresid (default 1) is used for the RESId numbering. See examples in test/c39test/readpdb.inp.
Top Reading coordinates The reading of coordinates is done with the READ COOR command, and there are several options (which may change over in future versions). Coordinates may be read into the main set or the comparison coordinate set using the COMP keyword. There are three possible file formats that can be used to read in coordinates. They are coordinate binary files, dynamics coordinate trajectories, and coordinate card images. In addition, NAMD program binary restart coordinates(and velocities) files can be read (only into main set). Protein Data Bank (PDB) formatted files can also be read. PDB files do however require some editing first. All the HEADER and other junk before the actual coordinate section has to be removed and optionally replaced by a standard CHARMM title. There should be no line with NATOM (= number of atoms) preceding the actual coordinates. would either have to rename some entries in the PSF or in the coordinate file in case there are differences. The MODEL option reads the specified MODEL number from an NMR style multiple coordinate set PDB file. For all formats, a subset of the atoms in the PSF may be selected using the standard atom selection syntax. For binary files, This is a risky maneuver, and warning messages are given when this is attempted. Only coordinates of selected atoms may be modified. When reading binary files, or using the IGNOre keyword, coordinate values are mapped into the selected atoms sequentially (NO checking is done!). Selection of atoms does not work with NAMD binary files (example: read namd file "myfile.coor.rst" The reading of the first two file formats is specified with the FILE option. The program reads the file header to tell which format it is dealing with. The coordinate binary files have a file header of 'COOR' and contain only one set of coordinates. These are created with a WRIT COOR FILE command. The dynamics coordinate trajectories have a file header of 'CORD' and have multiple coordinate sets. These files are created by the dynamics function of the program. To specify which coordinate set in the trajectory to be read, the IFILE option is provided. One specifies the coordinates position within the file. The default value for this option will cause the first coordinate set to be read. If the IFILE value is negative, then the next file (other than the first one) will be read. This will only work if a set has already been read from the file with a positive IFILE value. The CONTinue keyword specifies that frame counting will continue from the current position in the file, not from the start. The sequence READ COOR FILE IFILE 10 UNIT 51 READ COOR FILE CONT IFILE 10 UNIT 51 will first read frame 10 and then frame 20 from unit 51. In this way possibly expensive re-reading of the file from the beginning every time is avoided. For binary files, the APPEnd command will 'deselect' all atoms up to the highest one with a known position. This is done in addition to the normal atom selection. This is useful for structures with several distinct segments where it is desireable to keep separate coordinate modules. The CARD file format is the standard means in CHARMM for providing a human readable and writable coordinate file. The format is as follows: * Normal format for less than 100000 atoms and PSF IDs with less than five characters title NATOM (I5) ATOMNO RESNO RES TYPE X Y Z SEGID RESID Weighting I5 I5 1X A4 1X A4 F10.5 F10.5 F10.5 1X A4 1X A4 F10.5 * Expanded format for more than 100000 atoms (upto 10**10) and with upto 8 character PSF IDs. (versions c31a1 and later) title NATOM (I10) ATOMNO RESNO RES TYPE X Y Z SEGID RESID Weighting I10 I10 2X A8 2X A8 3F20.10 2X A8 2X A8 F20.10 The title is a title for the coordinates, see *note syn: (usage.doc)Syntactic Glossary, for details. Next comes the number of coordinates. If this number is zero or too large, the entire file will be read. Finally, there is one line for each coordinate. ATOMNO gives the number of the atom in the file. It is ignored on reading. RESNO gives the residue number of the atom. It must be specified relative to the first residue in the PSF. The OFFSet option should be specified if one wishes to read coordinates into other positions. The APPEnd option adds an additional offset which points to the the residue just beyond the highest one with known positions. This option also 'deselects' all atoms below this residue (inclusive). For example, if one is reading in coordinates for the second segment of a two chain protein using two card files, and the APPEnd option is used, RESNO must start at 1 in both files for the file reading to work correctly. It should also be remembered that for card images, residues are identified by RESIDUE NUMBER. This number can be modified by using the OFFSet feature, which allows coordinates to be read from a different PSF. Both positive and negative values are allowed. The RESId option will cause the residue number field to be ignored and map atoms from SEGID and RESID labels instead. RES gives the residue type of the atom. RES is checked against the residue type in the PSF for consistency. TYPE gives the IUPAC name of the atom. The coordinates of an atom within a residue need not be specified in any particular order. A search is made within each residue in the PSF for an atom whose IUPAC name is given in the coordinate file. The RESId option overrides the residue number and fills coordinates based on the SEGID and RESID identifiers in the coordinate file. This is the recommended method where different PSF's are used. The IGNORE option allows one to read in a card coordinate file while bypassing the normal tests of the residue name, number, and atom name. When IGNORE is specified in place of card, the identifying information is ignored completely. Starting from the first selected atom, the coordinates are copied sequentially from the file. The PDB option works very much like the CARD option, but expects the actual file format to be according to Protein Data Bank standards: text IATOM TYPE RES IRES X Y Z W A6 I5 2X A4 A4 I5 4X 3F8.3 6X F6.2 The OFFI option enforces the official pdb format. The segid (chain id) has to be one character in length on read and it is truncated to one character on write. Normally, the coordinates are not reinitialized before new values are read, but if this is desired, the INITialize keyword, will cause the coordinate values for all selected atoms to be initialized. Note that only atoms that have been selected, will be initialized (9999.0). The COOR INIT command provides a more general way to initialize coordinates. The READ COOR DYNR variant reads a full coordinate set from a dynamics RESTart file. It REQUIRES a matching PSF and allows no selections or other manipulations. A restart file (usually) contains three sets of atom data, and you chose which one to read in with keywords: CURR the current coordinates DELT the displacement to be taken from the current coordinates VEL the current velocities (in AKMA units) NOTE: The restart file written after a crash may be sligthly different, at present (c28a2) it contains the previous coordinates instead of velocities. The READ COOR TARG and READ COOR TAR2 commands read in the coordinates of the target for Targeted Molecular Dynamics (TMD; see tmd.doc)
Top Reading coordinates from nonstandard formats The reading of coordinates is done with the READ COOR command, and there are several options. One such option is the READ COOR UNIVersal command which will read using a previously specified format. The Universal format is specified by the READ UNIVersal command. This reads the specification from the input stream or from a specified file. READ UNIVersal The following commands clear the translation table and sets up default specifications for the file format. CHARMM - setup standard CHARMM format (default) PDB - setup brookhaven format AMBER - setup standard AMBER format UNKNown - setup null format (everything must be specified) The following commands specify the field locations of various items When reading free-of-field, the starting values are sorted to determine the ordering of parsing. SEGID start length RESID start length TYPE start length RESN start length IRES start length ISEQ start length X start length Y start length Z start length W start length The following commands specify how input lines should be considered. PICK start length string - choose only line that match one or more of these EXCL start length string - exclude any line that contains one of these TITL start length string - add any line containing one of these to the title The following commands specify character translation upon reading the file. TRANslate { SEGID external-segid internal-segid } { RESID external-resid internal-resid match-segid } { RESN external-resn internal-resn match-segid } { TYPE external-type internal-type match-resn match-segid } END - terminate reading universal file format
Top The Format of Parameter Files [SYNTAX Parameter read command format] READ { PARAmeter { CARD [PRINt] [APPEnd] [FLEX] } } { { [FILE] [NBON ] [MMFF] } } The CARD/FILE keywords specify a card (readable) or binary file format. The PRINT and NBON options determine the extend of printing while reading parameters. The NBON will list the NATVDW*(NATVDW+1)/2 vdw table. The APPEnd keyword will add the new paramters to the existing parameter set. APPEnd does not work with binary files, MMFF, CFF, SPAS. Also, only paramters of the same type (e.g. both FLEXible) may be appended. The MMFF keyword invokes the Merck Force Field paramter reader. see *note MMFF (mmff.doc). The FLEX keyword specifies the new flexible parameter format. This is the same as the standard CHARMM parameter format, but; (1) allows general wildcarding for all terms (2) allows parameter substitution for missing paramters (3) does not require a previously read RTF (no global MASSES list required) (4) allows the definition of paramter equivalence groups. [SYNTAX Parameter file format] Parameters can be read from cards or binary modules by the routine PARRDR. After the title, card file data is divided into sections beginning with a keyword line and followed by data lines read free field: ATOM (Flexible paramters only) MASS code type mass (Flexible paramters only) EQUIvalence (Flexible paramters only) group atom [ repeat(atom) ] (Flexible paramters only) BOND atom atom force_constant distance ANGLe or THETA atom atom atom force_constant theta_min UB_force_constant UB_rmin DIHE or PHI atom atom atom atom force_constant periodicity phase IMPRoper or IMPHI atom atom atom atom force_constant periodicity phase CMAP atom atom atom atom atom atom atom atom resolution <...cmap data...> NBONd or NONB [nonbond-defaults] atom* polarizability e vdW_radius - [1-4 polarizability e vdW_radius] NBFIX atom_i* atom_j* emin rmin [ emin14 [ rmin14 ]] HBOND [AEXP ia] [REXP ir] [AHEX ih] [AAEX iaa] [hbond-defaults] donor-heavy-atom* acceptor-heavy-atom* well_depth distance ( SPAS only paramter types ) FLUC atom chi_value zeta_value prin_integer chma_value KAPPa atom atom atom atom atom atom force_constant LCH2 atom atom atom atom atom force_constant 14TG atom atom atom atom trans_const gauche_const PRINt [ON ] [OFF] where '*' allows wildcard specifications: * matches any string of characters (including none), % matches any single character, # matches any string of digits (including none), + matches any single digit. --------------------------------------------------------------------------- nonbond-defaults::= [NBXMod int] [CUTNB real] [CTOFNB real] [CTONNB real] [WMIN real] [E14Fac real] [EPS real] [ATOM ] [CDIElectric] [SHIFt ] [VATOm ] [VSWItch ] [BYGRoup] [GEOMetric ] [GROUp] [RDIElectric] [SWITch ] [VGROup] [VSHIft ] [BYCUbe ] [ARIThmetic] [FSWITch] [VFSWitch] [FSHIft ] hbond-defaults::= [ ACCEptor ] [ HBEXclude ] [ BEST ] [ NOACceptor ] [ HBNOexclude ] [ ALL ] [CUTHB real] [CTOFHB real] [CTONHB real] [CUTHA real] [CTOFHA real] [CTONHA real] [REXP int(def12)] [AEXP int(def10)] [HAEX int(def4)] [AAEX int(def2)] --------------------------------------------------------------------------- Sections end with the occurence of the next keyword line, or a line with the word END, the latter terminating parameter reading. Errors in the input file will result in warning messages but not termination of the run. For angles, if theta_min is given as a negative number, then a cosine style angle potential function being used for those angles, rather than CHARMM's usual angle potential energy function. No wildcard usage is allowed for bonds and angles. For dihedrals, two types are allowed; A - B - C - D (all four atoms specified) and X - A - B - X (only middle two atoms specified). Double dihedral specifications may be specified for the four atom type by listing a given set twice. When specifying this type in the topology file, specify a dihedral twice (with nothing intervening) and both forms will be used. There are five choices for wildcard usage for improper dihedrals; 1) A - B - C - D (all four atoms, double specification allowed) 2) A - X - X - B 3) X - A - B - C 4) X - A - B - X 5) X - X - A - B When classifying an improper dihedral, the first acceptable match (from the above order) is chosen. The match may be made in either direction ( A - B - C - D = D - C - B - A). The periodicity value for dihedrals and improper dihedral terms must be an integer. If it is positive, then a cosine functional form is used. Only positive values of 1,2,3,4,5 and 6 are allowed for the vector, parallel vector and cray routines. Slow and scalar routines can use any positive integer and thus dihedral constrains can be of any periodicity. Reference angle 0.0 and 180.0 degree correspond to minimum in staggered and eclipsed respectively. Any reference angle is allowed. The value 180 should be prefered over -180 since it is parsed faster and more accuratly. When the periodicity is given as zero, for OTHER THAN THE FIRST dihdral in a multiple dihedral set, then a the amplitude is a constant added to the energy. This is needed to effect the Ryckaert-Bellemans potential for hydrocarbons (see below). The normal dihedral energy equation is: E = K * ( 1.0 + cos( periodicity * phi - phase ) ) When the periodicity is given as zero, then a harmonic restoring potential in (phi - phi_min) is used. The phase value gives phi_min for this option. This functional form is identical to that reported in the CHARMM paper, except that either functional form (referred to as proper and improper) may be used for dihedrals and improper dihedrals. The distinction between these terms is that seperate lookup tables are kept and the default atom choices are still different. For dihedrals, the selection is usually based on the middle two atoms, and for improper dihedrals, the selection is based on the outer two atoms. For either terms, all 4 atoms may be required. The HBOND line can be used to specify exponents for the hbond function, with ia and ir being the attractive and repulsive radial terms and ih and iaa the cosine exponents on the angular terms at the h and a respectively. Defaults 4, 6, 4, and 2 respectively. For atom types with no NBOND parameters given, no van der Waals interactions will be calculated. You will be warned, but be careful. The nbond parameters for 1-4 interactions can be specified by placing the extra set of parameters after the first. By default the same parameters will be used for 1-4 and all other interactions. NON-BOND parameter combination rules depend on how the parameters are listed. If the second number is negative, it is used as Emin, and Emin(ij)=-sqrt(Emin(i)*Emin(j)). If the second number is positive, it is used as Neff, and the Slater Kirkwood formula is used to compute Emin(ij). The PARRDR card field ,NBFIX, allows individual atom type van der Waal pair interactions to be specified. Subsequent lines must have; atom_i atom_j emin rmin [ emin14 [ rmin14 ]] If emin is positive, a severe warning is issued. The wildcard "X" may be given. In the case where both atoms are wildcards, the entire nbond parameter set will be modified. If emin14 and rmin14 are not specified, then the value of emin and rmin will be used. NOTE: The previous value will not be used. NBFIXes are processed in order. For that reason, wildcard usage should come first. In the case of duplicate specifications, there is no check, and the last specification will be used. The maximun number of NBFIX entries is currently set at 150. The space for this is allocated in PARMIO. PARAMETER I/O ADDENDUM: In order to calculate the Ryckaert-Bellemans torsional potential for butane and other extended atom hydrocarbons, the following terms should be included in the parameter file: V = gamma[1.116 - 1.462cos(phi) - 1.578 cos**2(phi) + 0.368 cos**3(phi) + 3.156 cos**4(phi) - 3.788 cos**5(phi)] and gamma = 1.987 kcal/mol J. P. Ryckaert and A. Bellemans, Chem. Phys. Lett. 30, 123 (1975). J. P. Ryckaert and A. Bellemans, Disc. Farad. Soc. 66, 95 (1978). PHI ! Ryckaert Bellemans has trans = 0.0 ! since cos is an even function cos(-phi)=cos(phi), invert the ! sign of the coefficients with odd power of cos(phi) CH3E CH2E CH2E CH3E 0.470467 5 0.0 CH3E CH2E CH2E CH3E 0.783947 4 0.0 CH3E CH2E CH2E CH3E 2.53516 3 0.0 CH3E CH2E CH2E CH3E 1.56789 2 0.0 CH3E CH2E CH2E CH3E 2.34787 1 0.0 CH3E CH2E CH2E CH3E -4.70368 0 0.0 The potential should be used with SHAKE bonds and angles or bonds only as required. The zero periodicity (constant) term should NOT be the first in the set, otherwise it will be treated as an improper torsion.
Top [SYNTAX RTF file format] The Format of a Residue Topology File Here is a description of what is currently (24-May-1982) in residue topology files (as they are stored in ascii files). You may use this format if you specify the CARD option in the READ command. The format of binary files depends on the current implementation of the RTF data structure (see RTF.FCM). The purpose of residue topology files is to store the information for generating a representation of macromolecule from its sequence. These files are read by RTFRDR a subroutine in RTFIO which should be be consulted for formats and the final word on what is actually done with these files. The residue topology files are named TOP... . There are two forms, binary module (.MOD) and card format (usually .INP or .RTF) although the binary is typically no longer used. The card format files are structured as input files for CHARMM, beginning with a run title and the command READ RTF CARD, followed by the actual topology file. The first section of the topology files is a title section in the usual format of up to ten lines delimited by a line containing only a * in column 1. The remaining information is read in free field format as commands to define the RTF. The ordering of the commands is important in that some information is needed to define others (i.e. the atoms of a residue must be defined before the bonds between them). The recommended structure of this file is: Initial setup: MASS specification for each atom type DECLarations of out of segment definitions DEFAults for patching on the fist and last residues AUTOgenerate angles dihedrals patch For each residue: RESIdue name and total charge specification (or PRESidue if this is a patch) ATOM definitions within this residue GROUping dividers between atom definitions BOND specification ANGLe specifications DIHEdral angle specifications IMPRoper dihedral angle specifications CMAP dihedral angle specifications, resolution DONOr specifications ACCEptor specifications IC information PATChing residues to use if defaults are not desired Closing: END statement Display control: PRINT option The format above is not rigid. In particular, The 'out of residue declarations' may be augmented and redefined at any point. These declarations are checked against all 'out of segment' atom references. This is done to avoid potential problems where atom names are misspelled. The number following the declaration is ignored, and is for the users own reference (or debugging). The syntax of all subcommands are as follows: MASS atom-type-code atom-type-name mass As of c40a1 the atom-type-code can be input as a -1 and this generates atom-type-codes internally in a sequential manner defining the atom-type-code for the current mass declaration as that which increments NATC by one. One can mix both explicitly specified atom-type-codes and -1 values, the atom-type-codes are generated internally based on the atom-type-name. DECLare out-of-residue-name This adds names to be considered for possible connections to the previous or next residues. This is done as a spelling check. Any atoms names not contained with in the residue nor on this list of declarations will be flagged as an error. Use the symbol "-" as an atom name prefix to denote the previous residue, use "+" for the subsequent residue. Use "#" as a prefix for the (n+2) residue. DEFAults [ FIRSt { name } ] [ LAST { name } ] { NONE } { NONE } AUTOgenerate [ ANGLes ] [ DIHEdrals ] [PATCh] [DRUDe] [NOANgles] [NODIhedrals] [OFF] { RESIdue } name [total-charge] { PRESidue } Residues labled PRES may only be used for patching. Residues defined with RESI may not be used as a patch. ATOM iupac atom-type-name charge repeat(exclusion-names) GROUp This keyword divides the structure into specific electrostatic groups. These are used with explicit group-group electrostatic options and are used to make the atom-atom list generation more efficient. If a RESIdue does not start with a GROUp command, then any ATOMs defined will belong to the last group of the previous residue. Also, the maximum number of atoms allowed in any group is currently set at 1000 (MAXING in dimens.fcm). As a general guide, and electrostatic group should be roughly neutral or have unit charge. A group should generally be a rigid group of atoms, and should not have heavy (non-hydrogen) atoms in a 1-5 arrangement. Hydrogens should always be in the same group as its bonded partner. A group should NEVER include two or more groups of atoms that are not covalently linked. BOND repeat(iupac iupac) { ANGLe } repeat(iupac iupac iupac) { THETa } { DIHEdral } repeat(iupac iupac iupac iupac) { PHI } { IMPRoper } repeat(iupac iupac iupac iupac) { IMPHi } { CMAP } repeat(iupac iupac iupac iupac iupac iupac iupac iupac) DONOr [ hydrogen ] [ heavy-atom ] [ antecedent-1 antecedent-2 ] [ BLNK ] [ hydrogen ] The antecedents are not required unless hydrogen position generation is desired. ACCEptor iupac [iupac [iupac] ] The first antecedents is required if and angle dependence about the acceptor atom is desired. The second antecedent is unused. { IC } { BILD } name name name name bond angle phi angle bond { BUILd } BLNK may be used to indicate a missing atom name. DELEte { ATOM } iupac [COMBine iupac] { BOND } (iupac iupac) { THETa | ANGLe } (iupac iupac iupac) { DIHEdral | PHI } (iupac iupac iupac iupac) { IMPHi | IMPRoper } (iupac iupac iupac iupac) Deletions are allowed only in patch residues (PRES); the optional COMBine keyword for ATOM deletions allows passing part of the IC data for the deleted atom to the "combine" atom, i.e. stereochemistry of atoms bonded to the deleted atom. In order to use the COMBine option, both atoms must be present in the PSF and it must be invoked from the PATCh command (not the GENErate command). PATChing [ FIRSt { name } ] [ LAST { name } ] { NONE } { NONE } PRINt { ON } { OFF } The PRINt command may be used to control the display of lines as they are read by the RTF reader. The initial setting for printing is controlled by the READ command itself. If PRINT is specified, then printing will initially be enabled; otherwise, the commands will not be echoed. PRINT ON turns on echoing of RTF specifications; PRINT OFF turns them off. This command is useful for debugging an addition to a previously tested topology file. A small sample RTF card file follows: * title for documentation example 18 1 MASS 1 H 1.00800 MASS 11 C 12.01100 MASS 12 CH1E 13.01900 MASS 13 CH2E 14.02700 MASS 14 CH3E 15.03500 MASS 31 N 14.00670 MASS 38 NH1 14.00670 MASS 51 O 15.99940 MASS 56 OH2 15.99940 DECL -C DECL -O DECL +N DECL +H DECL +CA DEFA FIRS NTER LAST CTER RESI ALA 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH3E 0.00 GROU ATOM C C 0.45 ATOM O O -0.45 BOND N CA CA C C +N C O N H BOND CA CB THET -C N CA N CA C CA C +N THET CA C O O C +N -C N H THET H N CA N CA CB C CA CB DIHE -C N CA C N CA C +N CA C +N +CA IMPH N -C CA H C CA +N O CA N C CB CMAP -C N CA C N CA C +N DONO H N -C CA ACCE O C BILD -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 BILD -C N CA C 0.0000 0.00 180.00 0.00 0.0000 BILD N CA C +N 0.0000 0.00 180.00 0.00 0.0000 BILD +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 BILD CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 BILD N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 RESI OH2 0.00000 GROUP ATOM OH2 OH2 -0.40000 H1 H2 ATOM H1 H 0.20000 H2 ATOM H2 H 0.20000 BOND OH2 H1 OH2 H2 THET H1 OH2 H2 DONO H1 OH2 -O -O DONO H2 OH2 -O -O ACCE OH2 PATC FIRS NONE LAST NONE END NOTES:: The use of improper dihedrals for the PSF is unrelated to the use of improper dihedrals for the internal coordinate tables. L PSF usage: | | I / \ / \ -----J---- K------ IC table usage: I L \ / \ / *K | | J Note that for PSF usage the first atom is the central atom, and the last atom is the atom to be restained relative to the axis defined by the middle pair of atoms. For the IC table usage, the central atom is in the third position, but the axis is again defined by the middle pair of atoms. Also note that as of c40a the atom-type-code that follows the MASS statement in the RTF (as described above for the PARAMETER file) can be given as -1, which will cause a sequential atom-type-code, array ATCT in the RTF, to be placed at NTCT+1, where NTCT is the value of the largest atom-type-code specified to date.
Top Reading data other than the sequence or coordinates The parameter files (PARA) and internal coordinate files (IC) and hydrogen bond (HBONd) data files can be read as card images or binary files. Specifying CARD signifies card image input; specifying FILE signfies binary file input. Please note that topology file must be read in before the parameters can be read. Protein structure files (PSF) files can be read and written in card/ascii format either with the "old" CHARMM format of using the "XPLOR" format, which replaces the atom-type code with the atom type name. This has been implemented both for ascii (card) and binary (file) type reads/writes, but reading a binary (file) formated psf file is no longer supported in The non bonded list (NBONd) can only be read as a binary file. The constraints (CONStraint) which includes dihedral restraints may only be read as formatted file (card). There are two types of IC card files (residue number vs. resid's). The residue number option is the default, and atom assignments are based on residue number. This is the low precision form. The resid option is the high precision form and atom assignments are based on SIGID's and RESID's. This is also useful where different homologies are used. The Image file (IMAGes) containing transformation information can only be read in card image format (see *note images:(images.doc).). The INIT keyword will remove all existing image data. Without the INIT keyword, any existing image items (such as bonds) would be kept. This allows one to modify the crystal geometry without the necessity of regenerating all image items. The TABLe file contains the nonbond energy lookup information. Once read in, The effects cannot be reversed. The nonbond energy evaluation is now under control of the table routines. The BTABle file contains the bonded energy lookup information. Once read in, the effects cannot be reversed. The bonded energy evaluation is now under control of the table routines. The table must be read after the structure (psf) of the system is set up. The format of the table is the following: BOND A B 104 1.86999999999998e+00 -3.74058562118872e+02 1.90794423875772e+02 1.88999999999998e+00 -3.66707803850426e+02 1.83386760216079e+02 ... Here 'BOND' is the type of the bonded interaction. The other choices are 'ANGLE' and 'DIHE', for angular and dihedral interactions. Second line 'A B' defines the two atom types between which the bonded interaction is set. For 'ANGLE' three atom types are required, and for 'DIHE' four atom types are required. Third line defines the number of entries in the lookup table. The lookup table itself starts on the fourth line with three real numbers per line. The first column is the distance between the atoms for 'BOND', or the angle in radians for 'ANGLE' and 'DIHE'. The second column is the gradient of the potential energy (-1 x force) and the third column is the potential energy. The NM file contains normal modes from previous *note DIMS:(dims.doc) runs. With the help of this file those modes can be avoided on subsequent runs, which increases the diversity of trajectories. This is part of the 'self avoidance' algorithm in the DIMS module and used with the DIMS keywords MTRA, NWIND, and NMUN.
Top WRITe - Writes Data Structures to External Files [SYNTAX WRITe] Syntax WRITe { { PSF } [FILE] } UNIT unit-number | NAME filename { [CARD] [XPLOr] } { { RTF } } { { PARAmeter } } { { NBONd }* } { { TABLe } } { } { { COORdinate coor-spec } [CARD] } { [PDB [MODEL int [FIRSt|LAST]] [OFFI]} { [DUMB] } { [XYZ] } { { IC [RESId] [SAVEd] } [FILE] [RTF]} { { HBONd [ANAL] } } { } { { IMAGes imag-spec} [CARD] } { { ENERgy } } { { CONStraint [PSF 0] } } { { TITLe } } title { NAMD FILE "filename" ** } ** no other options are available coor-spec:== [COMP] [OFFS int] [IMAGes] atom-selection imag-spec::= [ TRANsformations ] [ FORCes ] [ PSF ] *: The NBOND list can only be WRITten in binary (FILE) form. Use PRINt to get formatted output. Function The primary purpose of this command to save some of CHARMM's data structures. The coordinate and internal coordinate data structures can be written in formatted form so that they be edited independent of CHARMM using a text editor. The option, FILE, specifies that a file is to be written in unformatted form (binary). The option, CARD, specifies that a file is to written in formatted form. For the coordinate and internal coordinate file, CARD is the default. The coordinate option PDB gives a file in Protein Data Bank format, with just the ATOM records; the MODEL N option writes a PDB file in the NMR-style multiple coordinate set format (note that for this to work the file has to be specified as UNIT <int>, not as NAME <string>): MODEL 0 (or no MODEL keyword) just write standard PDB file MODEL 1 writes beginning of multicoordinate file (title, MODEL 1, coor, TER, ENDMDL) MODEL N (N>1) appends just coordinates for MODEL N (MODEL N, coor, TER, ENDMDL) MODEL N (N<0) appends last coordinate set, and END (MODEL |N|, coor, TER, ENDMDL, END) Keyword FIRSt forces writing of title even if N.NE.1, LAST forces writing of END line. The XPLOr option of WRITe PSF produces an XPLOR style PSF file (atom names are used instead of atom numbers) The selection of "PSF 0" in the WRITe CONS only works with PERT and writes data for the lambda=0 PSF. A set of title lines must follow the WRIT command. This title will be written at the start of the file and serves to document the file. For your protection, one should always make good use of this title, as it may be the only documentation for the file. The UNIT keyword specifes what Fortran unit the output should be written to. It cannot be omitted unless the filename is provided with the NAME keyword. The XYZ keyword writes a simple .xyz format file with (A8,3F11.5), as an export format for other programs; the first title line is used for the comment record.
Top PRINt - writes information to output file (unit 6) [SYNTAX PRINt] Syntax PRINt { PSF [XPLOr] } { RTF } { CONStraint [PSF 0] } { PARAmeter [USED] } { RESIdue } { COORdinate coor-spec } { IC [ SAVEd ] [RTF] } { HBONd [ ANAL ] } { NBOND } { IMAGes imag-spec } { TITLe } { ENERgy } coor-spec::= [COMP] [OFFS int] [IMAGes] atom-selection imag-spec::= [ TRANsformations ] [ FORCes ] [ PSF ] Syntactic ordering: All commands must be typed in the order shown. Function This command is used to list information contained in data structures used by the program. The information must already have been created through use of a READ, GENE, HBON, etc., command. The printable output is sent to unit 6. The XPLOr option of PRINt PSF produces an XPLOR type PSF listing. Atom names are printed instead of atom numbers. The selection of "PSF 0" in the PRINt CONS only works with PERT and prints data for the lambda=0 PSF. For printing paramters, the USED option causes the print of only the paramters that were used in the most recent energy evaluation. This option is PSF dependent. For hydrogen bonds, ANAL gives a geometrical and energy analysis of the hydrogen bonds. Representing the hydrogen bond as A2-A1-X-H....Y-, the distances X-Y, H-Y, the angle (180 - <X-H-Y ), the dihedral angle A2-A1-X-H and the hydrogen bond energy contribution are listed. A more versatile hbond analysis facility is provided by COOR HBOND (see *note corman:(corman.doc)).
Top [SYNTAX TITLe] Titles - Specifying and manipulating Titles are optional. All title lines MUST begin with a "*". If no title is specified, the title will be untouched. This is useful when a series of titles are needed. Titles are terminated with a line containing only a "*" in the first colunm. There may be up to 32 lines contained in any title. The titles are read using RDCMND, thus parameter substitutions are allowed. A command TITLe has been added to CHARMM which can be used to specify a title to be used by subsequent write commands. For interactive use, A title is always required (no backspace can be done) when RDTITL is called. The date,time, and user is added at the end of the title when a title is written to a file. If a date and time is already present, it will be superceeded. For the print option, the date and time information is left as it was. A second title array TITLEB has been added to CTITLA.FCM TITLEA is to be used for writing, and TITLEB must be used for reading from data files. In this way, the main title is never destroyed by reading a data file. For any write command, TITLEA can be modified by specifying a title. Any further writes will use that title, unless a new title is specified. As it is now, title lines should not end in "-" and any characters beyond a "!" will not be included in the title. Titles may begin with a "#" as well as "*". The pound sign is converted to a "*" upon reading. When the first title line begins with "#", the old title is not destroyed. All entered title lines superceed any previous title lines. Obviously, if more title lines are entered than were previously present, then there will be no difference in the two methods. This option was added for cases where a series of identical titles, except for a different first line, was needed. The COPY keyword of the TITLe command will copy the current TITLB (the reading title) to TITLA (the writing title) before reading the subsequent title. If there is no subsequent title, then just a copy is done. Normally, when titles are written to card files, the first column "*"s are retained. With the WRITe TITLe command, several changes are made. First, the first colunm of "*"s is suppressed. Second, no date and time and username is added. Third, the file is not closed. This command is primarily used for creating files for plotting. It is often used in conjunction with looping and energy terms. Here is an example of possible applications; OPEN WRITE CARD UNIT 23 NAME ENERGY.DAT ! Open the file for plot data WRITE TITLE UNIT 23 * this file contains ..... * more message data ..... SET 1 -180.0 ! Set the initial dihedral angle value LABEL LOOP ! Here is the loop return point CONS DIHE ....... MIN @1 ! Introduce the desired dihedral constraint MINIMIZE ..... ! Minimize CONS CLDH ! Remove the dihedral constraint SET 2 @1 ! copy parameter one to parameter two TRIM 2 FROM 1 TO 10 ! Pad parameter two with blanks for formatting ! It will now be 10 characters long WRITE TITLE UNIT 23 * DIHEDRAL = @2 ENERGY = ?ENER ! write this only this line to unit 23 INCREMENT 1 BY 15.0 ! Add 15 to parameter one IF 1 LT 180.1 GOTO LOOP CLOSE UNIT 23 STOP
Top I/O Format Control IOFOrmat [ EXTEnded | NOEXtended ] In c30a2, the PSF entries are extended for I10 atom numbers and character*8 PSF IDs (SEGID, RESID,RES and TYPE). Atom numbers take I5 in coordinate files and I8 in psf files and CHARACTER*4 PSF IDs are used for Normal (noextended) I/O operation. These are expanded to I10 and A8 respectively. Noextended format is the default and the extended format is used only when the number of atoms is greater than 100000 or any PSF ID is longer than 4 characters. The IOFOrmat command overrides the default: IOFOrmat EXTEnded enforces the extended format and IOFOrmat NOEXtended does the normal (old) format.