c40b1

parmfile

CHARMM Emprical Energy Function Parameters This section describes parameters in the CHARMM empirical energy function. * Overview / Overview of CHARMM parameter file * Multiple / Rules for the use of multiple dihedrals in CHARMM22 * Conversion / Rules for conversion of old nucleic acid rtf and param to CHARMM22 format * PARMDATA / Description of Parameter Files available for general use.
Top Overview of CHARMM parameter files By Alexander D. MacKerell Jr., July 1997 Updated; January 2010 This section of the documenation contains a brief description of the contents of a parameter file. The CHARMM parameter file contains the information necessary to calculate energies etc. when combined with the information from a PSF file for a structure. Information on the keywords found in the parameter file is in IO.DOC. (A) * CHARMM example parameter file * (B) BOND H O 500.0 1.00 (C) ANGLe (THETa) H O H 100.0 104.51 20.0 1.70 (D) DIHEdral (PHI) HT CT CT HT 10.0 3 180.0 X CT CT X 10.0 3 180.0 (E) IMPH O C CT N 5.0 1 0.0 X C CT X 5.0 1 0.0 X X CT N 5.0 1 0.0 O X X N 5.0 1 0.0 (F) CMAP CT1 N CT1 C N CT1 C CT1 24 cmap data: 2D array of energy correction values (G) NBONDed nonbond-spec H 0.00 -0.046 0.2245 0.00 -0.023 0.2245 O 0.00 -0.120 1.8000 0.00 -0.060 1.8000 (H) NBFIX H O -0.30 1.50 -0.15 1.50 (I) HBONDs hbond terms (IO.DOC) H O -0.00 1.00 (J) END The parameter file starts with a title (A) which contains information on the origins and applicability of that file. Section (B) BONDs, contains information on all bond force constants and equilibrium geometries. In this as well as the remainder of the parameter file the bonds etc. are specified by the atom type associated with each IUPAC atom in the topology file. Section (C) ANGLes or THETas, are specified by 3 atom types followed by the force constant and equilibrium geometry. If a Urey-Bradley term is desired between the 1 and 3 atom types of the angle a second U-B force constant and equilibrium geometry are included. If the equilibrium geometry is given as a negative number, then a cosine based angle energy function is used instead of NOT supported for the cosine based angle potential. Section (D) DIHEdrals (PHI), contains the 4 atom types specifing a dihedral followed by the force constant, the multiplicity of the dihedral and the minimium geometry of the dihedral. With dihedrals wildcards, X, as shown may be included for the terminal atoms. Also, multiple dihedrals of different multiplicities may be specified for a single dihedral as outlined below. As of version 25 any value of the phase (besides 0 and 180) is possible. However, the use of phases other than 0 and 180 is discouraged, as the resulting potential is asymmetric, and hence unphysical in most (if not all) cases. See io.doc for more information. Improper dihedrals (E) IMPH, used for out of plane motions are specified in the same fashion as dihedrals. The use of wildcards, X, is also allowed in a number of variations. Multiple improper dihedrals are not supported. Ordinarily, improper dihedrals are given a multiplicity of 0, which imposes a harmonic restoring potential instead of a cosine function. In this case, the central atom must be either the first or the last atom in the definition, else the resulting potential will be asymmetric and exhibit a discontinuity at equilibrium! By convention, the first atom of an improper dihedral (type A-X-X-B or A-B-C-D) should be the central atom. See io.doc for more information. Cross-term energy correction map, CMAP (F), is a 2D grid correction where the 2 dimensions correspond to two dihedral angles, where the first four atom types correspond to the first dihedral and the next four atom types to the second dihedral angle. A CMAP specification is required in the topology file (see rtop.doc) and properly generated for this energy term to be applied. The integer following the 8 atom types represents the dimensions of the 2D grid. In the present example, 24 indicates that for the 360x360 deg surface, grid data in 15 deg increments is being used. The data in the CMAP grid is presented starting from -180 down to 0 and then increased to the final value (165 for the present example). Parameters for (G) NONBonded VDW parameters may be specified in two ways. Initially the Tanford-Kirkwood Formula was used where the atom polarizabilities, Number of effective electrons, and (minimum radius)/2 were required. In this formulation the first term following the atom type is the atom polarizability, the second term is the number of effective electrons and must be positive in order to specify the Tanford-Kirkwood Formula and the third term is the (minimum radius)/2. If the second term is negative, then the first number is ignored, the second term is the well-depth (epsilon) and the third term is the (minimum radius)/2. Both formulations use the Lennard-Jones 6-12 formula to determine the VDW interactions, in the first method the Tanford-Kirkwood Formula is used to calculate the well-depth (epsilon) and in the second method it is used directly. With both formulations a second set of 3 numbers may be specified to indicate the VDW parameters to be used for the calculation of 1-4 nonbonded interactions. Wildcards (*, %, etc. see MISCOM.DOC) may be used with the NONBond as well as the NBFIX and HBOND sections of the parameter file. The NBFIX section (H) allows VDW interactions between specific atom pairs to be modified. This is done by specifing the 2 atom types followed by the well depth and the minimum radius (not (minimum radius)/2 as in NBOND). A second well depth and minimum radius may be specified to determine the 1-4 interactions. The final section (I) contains the hydogen bond well depths and minimum radii for various atom pairs. In current versions of the parameters) hydrogen bonding is included implicitly in the electrostatic and VDW interactions. Thus, the HBOND well depth is set to -0.00 and in most calculations IHBFRQ should be set to 0 to avoid updating the hydrogen bond lists. This facility is still supported to allow calculations using the Lennart Nilsson nucleic acid parameters, AMBER parameters and for analysis of hydrogen bond geometries. It should be noted that both the NBOND and HBOND keywords are followed by a number of keywords dictating truncation schemes, 1-4 interaction treatments and dielectric constants, amoung others. These specifications are of the upmost importance for relabile calculations and deviations from the default values supplied with the parameter files should be done with the utmost caution. As of version 27, a special parameter files, par_hbond.inp, was added to the toppar directory; it contains information to calculated hydrogen bonds. Note that the resulting energetics are meaningless and are only included to aid in the analysis of hydrogen bonds.
Top Rules for the use of multiple dihedrals in CHARMM24 1) The association of 1 or more dihedrals with different multiplicities to a specfic dihedral type (as specified by atom types) is specified by the presence of 2 or more dihedral parameters in the parameter file. When multiple dihedrals are read in the parameter file and if the warning level (wrnlev) is 6 or more CHARMM will list those dihedrals in the output file (Note: the following type message "PARRDR> Multiple terms for dihedral type: INDEX 427 CODE31141959 CT3 -OS -CD -OB" indicates that the multiple dihedral has been successfully read). 2) If dihedral angles are AUTOGENERATED, then the RTF should not specify them again. Additional dihedrals in the RTF will be ignored and warnings given. 3) Without AUTOGENERATE, each dihedral should appear only once in the RTF. Multiple listings of a dihedral will be ignored and warnings given. 4) The order of the multiple dihedral entries associated with a specific dihedral is important; they must be placed sequentially in the parameter file. If they are not sequential errors will be given. This is new in C24B1 and later versions. For example: P ON2 P2 ON2 0.03 2 0.0 P ON2 P2 ON2 0.03 3 0.0 will place both a 2-fold and a 3-fold term on the P-ON2-P2-ON2 dihedral. 5) Wildcards may be used in the parameter file to specify multiple dihedrals(ie. X C1 C2 X), however, all the dihedrals in the parameter file associated with that dihedral type must be wildcards. Use of wildcards with multiple dihedrals is NOT recommeded. 6) Specific dihedral entries always override wildcard entries. For example: X C2 C3 X 100.0 1 180.0 C1 C2 C3 C4 100.0 2 180.0 X C2 C3 X 100.0 3 180.0 will assign the 2-fold term to C1-C2-C3-C4 while 1-fold and 3-fold terms would be assigned to C5-C2-C3-C6 and any other dihedral centered about the C2-C3 bond. This assignment of the multiple terms to a number of dihedrals is why the use wildcards for the specification of multiple dihedrals in NOT recommeded. The preferred method is as follows: X C2 C3 X 100.0 2 180.0 C5 C2 C3 C6 100.0 1 180.0 C5 C2 C3 C6 100.0 3 180.0 will assign the 1-fold and 3-fold terms to C5-C2-C3-C6 and the 2-fold term to C1-C2-C3-C4 and any other dihedral centered about the C2-C3 bond. This limits the potential for multiple dihedrals being mistakenly assigned to a dihedral centered on the C2-C3 bond. Thus, it is advised that when creating a multiple dihedral all 4 atom types be explicitly stated and, if necessary, new atom types be created to avoid conflicts. 7) This design is such that previous CHARMM topology and parameter files for proteins are compatible with CHARMM24. However, due to complexities in the multiple dihedral setup for the nucleic acid sugars (ribose and deoxyribose) the nucleic acid topology and parameter files are NOT compatible with CHARMM22. In order to make them compatible the following alterations must be performed. Alternatively, the altered files may be obained from Alexander D. MacKerell Jr.
Top Rules for conversion of old nucleic acid rtf and param to CHARMM22 format The following conversion rules apply to CHARMM22. Compatability with C24B1 and later versions will be insured if the multiple dihedrals in the converted parameters are sequential, as disscused above. ALL-HYDROGEN Protocol for conversion of all-hydrogen nucleic acid topology and parameter files (topnah*.inp and parnah*.inp) from a CHARMM21 or previous format to a format compatible with CHARMM22. This change is due to a new methodology for the treatment of multiple dihedrals in In Topology File (TOPNAH1.INP, TOPNAH1E.INP, TOPNAH1R.INP) 1) Create a new atom type, OSS 2) Convert the atom type of all O4' atoms to OSS In Parameter File (PARNAH1.INP) 1) Copy all OS parameters (bonds, angles, dihedrals etc.) and in the copy change OS to OSS. Be sure that the original OS parameter remains. Some OS to OSS copies can be avoided (such as OS P terms), however, one must be careful that all the necessary OSS parameters relating to O4' are present. Creating extra OSS parameters which are unused is not a problem. One exception occurs with the dihedral OS CH CH OS, where only one of the terminal OS atom should be converted to OSS. 2) In the DIHEDRAL (PHI) parameters under the heading "WILMA OLSON SUGAR MODEL" the following steps must be performed once all the OSS dihedral parameters are created. A) In all the explicit OS terms which don't include wildcards (X) or P atom types and have both 2 and 3-fold periodicities (2nd of 3 numbers following the dihedral) the 2nd 3-fold term must be commented out with a !. B) Of the new explicit OSS terms the following 3-fold terms must be commented out with a !. OSS CH CH OS 1.4000 3 0.0000 OH CH CH OSS 1.4000 3 0.0000 Lastly, when generating the structure be sure only the AUTOGENERATE ANGLE term is used. (i.e. do NOT use AUTOGENERATE DIHEDRAL). At this point the topology and parameter files should be compatible with CHARMM22 (but not CHARMM21 or a previous version of containing compound. In this test the energies should be calculated 1) using CHARMM21 or a previous version using the original, unmodified topology and parameter files and 2) with CHARMM22 using the modified OSS containing topology and parameter files. These energies should be equivalent. EXTENDED (UNITED) ATOM Protocal for the conversion of extended (united,explicit) atom nucleic acid topology and parameter files from CHARMM21 or previous format to a format compatible with CHARMM22. This change is due to a new methodology for the treatment of multiple dihedrals in CHARMM22. In Topology File (TOPRNA10 or TOPRNA10R) 1) Create 2 new atom types, OSS and OST 2) Convert the atom type of all O4' atoms to OSS except in the the patch PRES DEOX where it must be changed to atom type OST. This conversion to OST must also be performed in any residue, such as RESI DRIB, in which deoxyribose is used explicitly. 3) In the patch PRES DEOX add the line: ATOM O4' OST -0.30 ! (check the charge) before the GROUP statement and comment out the terms !DELETE DIHE O4' C4' C3' O3' ! WE NEED THIS AS A MULTIPLE TERM IN DEOXY !DIHE O4' C4' C3' O3' ! threefold !DIHE O4' C4' C3' O3' ! twofold such that no alterations in the dihedral setup are made. In Parameter File (PARDNA10.INP) 1) Copy all OS parameters twice (bonds, angles, dihedrals etc.); in the first copy change OS to OSS and in the second change OS to OST. Be sure that the original OS parameter remains. Some OS to OSS(OST) copies can be avoided (such as terms in which OS is adjacent to P), however, one must be careful that all the necessary OSS(OST) parameters relating to O4' are present. Creating extra OSS(OST) parameters which are unused is not a problem. One exception occurs with the dihedral OS CH CH OS, where only one of the terminal OS atom should be converted to OSS(OST). 2) In the DIHEDRAL (PHI) parameters under the heading "WILMA OLSON SUGAR MODEL" the following steps must be performed once all the OSS(OST) dihedral parameters are created. A) In all the explicit OS terms which don't include wildcards (X) or P atom types and have both 2 and 3-fold periodicities (2nd of 3 numbers following the dihedral) the 2nd term must be commented out with a ! (mostly 3-fold terms and 1 or 2 2-fold term). B) Of the new explicit OSS terms the following 3-fold terms must be commented out with a !. OSS CH CH OS 1.4000 3 0.0000 OH CH CH OSS 1.4000 3 0.0000 C) Maintain all of the OST dihedral terms. An example of the additions/alterations to pardna10.inp are listed below. BOND HO OSS 450.0000 0.9600 HO OST 450.0000 0.9600 OSS CH 292.0000 1.4300 OSS C2 292.0000 1.4300 OST CH 292.0000 1.4300 OST C2 292.0000 1.4300 C3 OSS 292.0000 1.38 C3 OST 292.0000 1.38 C OSS 292.0000 1.43 C OST 292.0000 1.43 THETA OSS C2 C3 150.5000 111.0000 OSS C2 CH 70.0000 112.0000 OSS C2 C2 82.0000 112.0000 OST C2 C3 150.5000 111.0000 OST C2 CH 70.0000 112.0000 OST C2 C2 82.0000 112.0000 C2 CH OSS 46.5000 111.0000 C2 CH OST 46.5000 111.0000 C3 CH OSS 46.5000 111.0000 C3 CH OST 46.5000 111.0000 CH CH OSS 46.5000 111.0000 CH CH OST 46.5000 111.0000 OSS CH NS 46.5000 111.0000 OSS CH NH2E 46.5000 111.0000 OST CH NS 46.5000 111.0000 OST CH NH2E 46.5000 111.0000 C2 OSS C2 82.0000 111.5000 CH OSS CH 46.5000 111.5000 HO OSS CH 46.5000 107.3000 HO OSS C2 46.5000 107.3000 C2 OST C2 82.0000 111.5000 CH OST CH 46.5000 111.5000 HO OST CH 46.5000 107.3000 HO OST C2 46.5000 107.3000 CH OSS C3 46.5 107.3 CH OST C3 46.5 107.3 C OSS C3 46.5 120.5 C OST C3 46.5 120.5 O C OSS 70.0 120.0 O C OST 70.0 120.0 CH C OSS 70.0 125.3 NA C OSS 70.0 120.0 CH C OST 70.0 125.3 NA C OST 70.0 120.0 OSS CH CS 46.5 111.0 OST CH CS 46.5 111.0 PHI X CH OSS X 0.9000 3 0.0000 X CH OST X 0.9000 3 0.0000 X C2 OSS X 0.5000 3 0.0000 X C2 OST X 0.5000 3 0.0000 ! OSS SUGAR TERMS OSS CH CH OS 0.5000 2 0.0000 !OSS CH CH OS 1.4000 3 0.0000 Should be commented out OH CH CH OSS 0.5000 2 0.0000 !OH CH CH OSS 1.4000 3 0.0000 Should be commented out OSS CH CH CH 0.5000 2 0.0000 OSS CH CH CH 1.4000 3 0.0000 OSS CH C2 CH 1.0000 2 0.0000 OSS CH C2 CH 1.4000 3 0.0000 OSS CH CH C2 1.4000 3 0.0000 OSS CH CH C2 0.5000 2 0.0000 OSS C2 C2 C2 1.4 3 0.0 OSS C2 C2 C2 0.5 2 0.0 ! OST SUGAR TERMS OST CH CH OS 0.5000 2 0.0000 OST CH CH OS 1.4000 3 0.0000 OH CH CH OST 0.5000 2 0.0000 OH CH CH OST 1.4000 3 0.0000 OST CH CH CH 0.5000 2 0.0000 OST CH CH CH 1.4000 3 0.0000 OST CH C2 CH 1.0000 2 0.0000 OST CH C2 CH 1.4000 3 0.0000 OST CH CH C2 1.4000 3 0.0000 OST CH CH C2 0.5000 2 0.0000 OST C2 C2 C2 1.4 3 0.0 OST C2 C2 C2 0.5 2 0.0 ! additional terms for tRNA OSS CH CS CF 1.5 3 0.0 OST CH CS CF 1.5 3 0.0 C2 CH C OSS 1.5 3 0.0 C2 CH C OST 1.5 3 0.0 X C OSS X 1.8 2 180.00 X C OST X 1.8 2 180.00 ! THE FOLLOWING TERMS UNDER THE HEADER ! "WILMA OLSON SUGAR MODEL": ! SHOULD BE COMMENTED OUT !OS CH CH OS 1.4000 3 0.0000 !OS CH CH CH 1.4000 3 0.0000 !OH CH CH OS 1.4000 3 0.0000 !OS CH C2 CH 1.4000 3 0.0000 !OS CH CH C2 0.5000 2 0.0000 !OS C2 C2 C2 0.5 2 0.0 IMPHI OSS X X CH 31.5000 0 35.2600 OST X X CH 31.5000 0 35.2600 CH OSS C2 NS 31.5000 0 35.2600 CH OSS CH NS 31.5000 0 35.2600 CH OSS C2 NH2E 31.5000 0 35.2600 CH OSS CH NH2E 31.5000 0 35.2600 CH OST C2 NS 31.5000 0 35.2600 CH OST CH NS 31.5000 0 35.2600 CH OST C2 NH2E 31.5000 0 35.2600 CH OST CH NH2E 31.5000 0 35.2600 NBONDED OSS 0.64 7.0 1.6 OST 0.64 7.0 1.6 Lastly, when generating the structure be sure only the AUTOGENERATE ANGLE term is used. (i.e. do NOT use AUTOGENERATE DIHEDRAL). At this point the topology and parameter files should be compatible with CHARMM22 (but not CHARMM21 or a previous version of containing compound. In this test the energies should be calculated 1) using CHARMM21 or a previous version using the original, unmodified topology and parameter files and 2) with CHARMM22 using the modified OSS containing topology and parameter files. These energies should be equivalent.
Top Description of topology and parameter files in version c31 and subsequent versions. In version 31 a major restructuring of the topology and parameter files was undertaken. This was performed to create a more modular approach to the files, thereby avoiding the problem of files becoming increasingly large. The restructuring was done such that the primary topology and parameter files for biomolecules can be used as they were previously. However, the topology and parameter information for the majority of model compounds used in the parameter development, additional molecules, including coenzymes, and patches parametrized to be compatible with the CHARMM force fields have been moved to toppar stream files. These toppar stream files have to be streamed in a and parameter files. They include both the topology and parameter information for the selected molecules, using the "read rtf card append" and "read param card append" commands to append the additional information to the topology and parameter lists. As of version c31 it is still necessary to maintain all the MASS atom lists in the parent topology and parameter files. Files in Version C35/C36 Topology files top_all22_prot.inp all hydrogen RTF for proteins, CHARMM22 with CMAP top_all35_carb.rtf all hydrogen RTF for sugars top_all32_lipid.rtf all hydrogen RTF for lipids with alkane dihedral update top_all36_lipid.rtf all hydrogen RTF for lipids (C36 and on) top_all27_na.rtf all hydrogen RTF for nucleic acids top_all32_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids top_all36_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids (C36 and on) top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids top_all32_prot_lipid.rtf all hydrogen RTF for proteins and lipids top_all36_prot_lipid.rtf all hydrogen RTF for proteins and lipids (C36 and on) top_all35_ethers.rtf all hydrogen RTF for ethers top_all30_cheq_prot.inp all hydrogen RTF for protein charge equilibration polarizable model toph19.inp extended atom RTF for proteins toprna10r_22.inp extended atom RTF for nucleic acids Parameter files par_all22_prot.inp all hydrogen parameters for proteins with CMAP par_all35_carb.prm all hydrogen parameters for sugars par_all32_lipid.prm all hydrogen parameters for lipids with alkane dihedral update par_all36_lipid.prm all hydrogen parameters for lipids (C36 and on) par_all27_na.prm all hydrogen parameters for nucleic acids par_all32_na_lipid.prm all hydrogen parameters for nucleic acids and lipids par_all36_na_lipid.prm all hydrogen parameters for nucleic acids and lipids (C36 and on) par_all27_prot_na.prm all hydrogen parameters for proteins and nucleic acids par_all32_prot_lipid.prm all hydrogen parameters for proteins and lipids par_all36_prot_lipid.prm all hydrogen parameters for proteins and lipids (C36 and on) par_all30_cheq_prot.inp all hydrogen parameters for protein charge equilibration polarizable model par_all35_ethers.prm all hydrogen parameters for ethers param19.inp extended atom parameters for proteins pardna10_22.inp extended atom parameters for nucleic acids (C) Toppar stream files (see stream subdirectory) listed under the parent topology and parameter files required for the individual files. Parent files: can be used with prot, na and lipid files toppar_dum_nobel_gases.str: dummy atom, helium and neon toppar_hbond.str: stream file to estimate hydrogen bond interactions Parent files: top_all22_prot.inp, par_all22_prot.inp (or top_all22_prot_cmap.inp, par_all22_prot_cmap.inp) toppar_all22_prot_model.str: model compounds used in protein parameter development as well as additional compounds toppar_all22_prot_aldehydes.str: small molecule aldehydes toppar_all22_prot_aliphatic_c27.str: extends all22 protein force field to include all27 alkane parameters toppar_all22_prot_fluoro_alkanes.str: optimized fluoroalkanes, requires toppar_all22_prot_aliphatic_c27.str toppar_all22_prot_heme.str: heme, O2, CO, CO2 and related patches toppar_all22_prot_pyridines.str: various substituted pyridines toppar_all22_prot_retinol.str: retinol, model compounds, Schiff's bases Parent files: top_all27_na.rtf, par_all27_na.prm toppar_all27_na_model.str: model compounds used in na parameter development including individual bases etc. toppar_all27_na_base_modifications.str: various chemical modifications of bases toppar_all27_na_carbocyclic.str: constrained bicyclic sugars toppar_all27_na_nad_ppi.str: NAD, NADH, ADP, ATP and others. Useful in combination with protein force field via the top_all27_prot_na.rtf and par_all27_prot_na.prm Parent files: top_all32_lipid.rtf, par_all32_lipid.prm toppar_all27_lipid_model.str: model compounds used in lipid parameter development, including alkenes toppar_all27_lipid_cholesterol.str: cholesterol and related model compounds Parent files: top_all36_lipid.rtf, par_all36_lipid.prm toppar_all36_lipid_model.str: model compounds used in lipid parameter development, including alkenes toppar_all36_lipid_cholesterol.str: cholesterol and related model compounds Parent files: top_all27_prot_na.rtf, par_all27_prot_na.prm toppar_prot_na_all.str: all compounds that require both protein and nucleic acid toppar information includes phosphorylated tyrosine, serine and threonine and some coenzymes (SAH) toppar_all27_na_bkb_modifications.str: various chemical modificaiton of the na backbone including abasic variants and phosphoramidate Parent files not needed toppar_water_ions.str: contains TIP3P water model and ions. All of these are also included in the prot, na and lipid topology and parameter files. toppar_amines.str: highly optimized neutral aliphatic amines. (D) Parameters for the polarizable force field based on a classical Drude oscillator. As this force field is currently under development such that the parameters have been placed in the "drude" subdirectory. Parameters for water, alkanes, ethers, aromatics, alcohols and amides are available as of January 2007 and this list will be expanding. See the 00readme for details and the approriate references. (E) Parameters for selected silicate and aluminosilicate surfaces have been developed. These parameters are designed to be compatible with the CHARMM22 and 27 force fields allowing for biological molecule-silicate surface interactions. As use of these parameters requires creation of the surface, which entails creation of the necessary patches, the parameters are included in the "silicates" subdirectory. This directory also includes examples and code to create the extended surfaces. See the 00readme file for more details. ref: Lopes, P.E.M., Murashov, V. Tazi, M. Demchuk, E. MacKerell, A. D., Jr. "Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface," Journal of Physical Chemistry B, 110: 2782-2792, 2006. (F) Additional topology and parameter files from various sources are included in subdirectories of the toppar directory. A description follows: non_charmm: Contains toppar files for AMBER, Bristol-Myers Squibb (BMS) and OPLS force fields along with a stream file for the SPC and SPC/E water models. These files have been tested to the extent that they may be considered reliable representations of the original force fields, though potentially not exact representations. These files are NOT maintained and, thus, use at your own risk. See the 00readme files and note that AMBER requires a special version of CHARMM as described in the 00readme file. tamdfff: An internal coordinate force field (ICFF) that was built based on the CHARMM 22 protein force field. Specifically, it provides a backbone covalent geometry suitable for torsion angle molecular dynamics (TAMD) and the necessary CMAP cross-term corrections to suppress distortions of the potential energy surface due to rigid covalent geometry. Additional details can be found in tamd.doc. Ref. J. Chen, W. Im and C. L. Brooks III, J. Comp. Chem. 2005, 26, 1565-1578. rush: A simple implicit-solvent protein force-field that adds terms to the bonded portion (bond + angle + dihe + impr + urey) of the all-atom the hydrophobic effect (_U_nburied _S_urface), and intra-molecular and protein-solvent hydrogen-bonding (_H_ydrogen-bonding) (hence _R_ _U_ _S_ _H_). Usage instructions are in doc/rush.doc gbsw: Optimized protein backbone parameters (par_all22_prot_gbsw.inp) and atomic input radii (radius_gbsw.str) for a balanced GBSW implicit solvent force field. The backbone phi/psi cross-term (CMAP) and the atomic input radii have been re-optimized specifically to balance the solvation and intramolecular interactions and to capture experimental conformational equilibria of both helical peptides and beta-hairpins. Additional information can be found in gbsw.doc. Ref. J. Chen, W. Im and C. L. Brooks III, J. Am. Chem. Soc. 128, 3728-36 (2006). Description of topology and parameter files prior to version c31. These files can be accessed via the toppar_history subdirectory of the toppar directory. (A) Topology files top_all22_prot.inp all hydrogen RTF for proteins top_all22_model.inp all hydrogen RTF for protein model cmpds top_all22_sugar.rtf all hydrogen RTF for sugars top_all27_na.rtf all hydrogen RTF for nucleic acids top_all27_lipid.rtf all hydrogen RTF for lipids top_all27_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids top_all27_prot_lipid.rtf all hydrogen RTF for proteins and lipids toph19.inp extended atom RTF for proteins toprna10r_22.inp extended atom RTF for nucleic acids (B) Parameter files par_all22_prot.inp all hydrogen parameters for proteins par_all22_sugar.prm all hydrogen parameters for sugars par_all27_na.prm all hydrogen parameters for nucleic acids par_all27_lipid.prm all hydrogen parameters for lipids par_all27_na_lipid.prm all hydrogen parameters for nucleic acids and lipids par_all27_prot_na.prm all hydrogen parameters for proteins and nucleic acids par_all27_prot_lipid.prm all hydrogen parameters for proteins and lipids param19.inp extended atom parameters for proteins pardna10_22.inp extended atom parameters for nucleic acids par_hbond.inp hydrogen bond parameters for analysis only Phased out: The CHARMM22 all-atom nucleic acid and lipid topology and parameter files are no longer included in the toppar directory due to their becoming obsolete. Note that they are included in the toppar_history directories. The CHARMM all-hydrogen topology and parameter sets may be considered to be stable, however, minor bug fixes may be performed as required. Additions may also occur leading to an expanding set of parameters which are compatible across proteins, nucleic acids, lipids, and, ultimately, carbohydrates. The carbohydrate(sugar) parameter work is still in progress by John Brady and coworkers; the number of sugar types should expand in the future. See the file toppar_all.history for a listing changes in the files over time. top_all22_model.inp includes the majority of model compounds used in the protein parameterization and is to be used in conjunction with par_all22_prot.inp. Three sets of combined topology and parameter files are included for use with 1) proteins and nucleic acids, 2) protein and lipids and 3) nucleic acids and lipids. In all cases the CHARMM22 protein parameters and the CHARMM27 nucleic acid or lipid parameters are used. The designation all27 for these files is based on the use of the most recent nucleic acid or lipid parameters. Test calculations using these combined files have yielded good results. Added as of July 1997 was the parameter file par_hbond.inp, which has been renamed to stream/toppar_hbond.str. This file is included for the analysis of hydrogen bonds; it includes information to calculate h-bond energies, but these are basically meaningless. The hydrogen bonds should NOT be used for energy, minimization and dynamics calculations with the CHARMM all-hydrogen topology and parameter sets. Ions in the all22 files are from two sources. Mg and Ca are from Prodhom and Karplus and were optimized specifically for the all22 parameters. The remaining cations are from Benoit Roux (see his thesis). They were optimized to be consistent with Param19, however, MD studies in a number of groups have shown them to work well. Note the presence of a variety of NBFIXES for the ions. These were initially optimized based on the proteins and later transferred to the lipids and nucleic acids based on analogy (by ADM Jr.). Ions in the all27 files have been optimized based on free energies of solvation by Roux and coworkers. As of August 1999 there were no NBFIXes used with these ions. The extended atom parameters for proteins are the same as those included with CHARMM20 which are based on Wally Reiher's thesis. They have been included in the supplement material of a recent publication (see suggested citations below). For the extended atom nucleic acid parameters those of Nilsson and Karplus, J. Comp. Chem. 7:591-616, 1986 are used which were also included in the CHARMM20 release and are the only set to include explicit hydrogen bonding terms. Some alterations of the extended atom nucleic acid topology and parameter files have been made in order to maintain compatibility with the multiple dihedral scheme in CHARMM22. Please send all remarks and suggestions to the CHARMM web page at www.charmm.org, Parameter Set Discussion Forum ADM Jr., July 2008 www.charmm.org or http://www.pharmacy.umaryland.edu/faculty/amackere/ References EXTENDED ATOM NUCLEIC ACID PARAMETERS Nilsson, L. and Karplus,M. Empirical Energy Functions for Energy Minimizations and Dynamics of Nucleic Acids J. Comp. Chem. 7:591-616, 1986 PARAM19 PROTEIN PARAMETERS Reiher, III., W.E. Theoretical Studies of Hydrogen Bonding, Ph.D. Thesis, Department of Chemistry, Harvard University, Cambridge, MA, USA, 1985 and Neria, E., Fischer, S., and Karplus, M. Simulation of Activation Free Energies in Molecular Systems, Journal of Chemical Physics, 1996, 105: 1902-21. MacKerell, J., A.D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R. L.; Evanseck, J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, I., W. E.; Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-hydrogen Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins using the CHARMM22 Force Field. Journal of Physical Chemistry B, 1998, 102, 3586-3616. CMAP 2D correction surface MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations, Journal of Computational Chemistry, 25: 1400-1415, 2004. FOR PHOSPHOTYROSINE Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D., and Lim, C. Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain-Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations, Journal of the American Chemical Society, 1996, 118: 11265-11277 Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data. 2000, 21: 86-104. MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA and RNA in Solution. 2000, 21: 105-120. Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids, Journal of Physical Chemistry B, 2000, 104: 7510-7515. Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids, Journal of Physical Chemistry B, 2000, 104: 7510-7515. Klauda, J.B., Brooks, B.R., MacKerell, A.D., Jr., Richard M. Venable, R.M. and Pastor, R.W., An Ab Initio Study on the Torsional Surface of Alkanes and its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer, Journal of Physical Chemistry B, 109; 5300- 5311, 2005 !above references and personal communication from the following Jeffery Klauda Joseph O'Connor Marcus Hadle Richard Venable J. Alfredo Freites Douglas Tobias Carlos Mondragon-Ramirez Igor Vorobyov Alexander D. MacKerell, Jr Richard W. Pastor POLYUNSATURATED LIPIDS Feller, S.E., Gawrisch, K. and MacKerell, Jr., A.D. "Polyunsaturated Fatty Acids in Lipid Bilayers: Intrinsic and Environmental Contributions to their Unique Physical Properties,: Journal of the American Chemical Society, 2002, 124:318-326 NAD+, NADH and PPI Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18: 221-239. MacKerell Jr., A.D., Wiorkiewicz-Kuczera, J. and Karplus, M. An all-atom empirical energy function for the simulation of nucleic acids, Journal of the American Chemical Society, 1995, 117:11946-11975. Patel, S., MacKerell, A.D., Jr., Brooks, C.L., III, CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model, Journal of Computational Chemistry, 25: 1504-1514, 2004 Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., Pastor, R.W., and MacKerell, A.D., Jr. "Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers," Journal of Chemical Theory and Computing, 3: 1120-1133, 2007 ! O-C-C-O torsion modified Hwankyu Lee, Richard M Venable, Alexander D MacKerell Jr., Richard W Pastor Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy Biophysical J., 95: 1590-1599, 2008 ! pyranose monosaccharides Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M., Pastor, R.W., MacKerell, Jr., A.D. “Additive empirical force field for hexopyranose monosaccharides” Journal of Computational Chemistry, 29: 2543-2564, 2008. PMID: 18470966 ! linear sugars, sugar alcohols, and inositol Hatcher, E., Guvench, O., and MacKerell, Jr., A.D. “CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol,” Journal of Chemical Theory and Computation, 5: 1315-1327, 2009, DOI: 10.1021/ct9000608. ! hexopyranose glycosidic linkages Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell, A. D. Jr. “Additive Empirical CHARMM Force Field for glycosyl linked hexopyranoses,” Journal of Chemical Theory and Computation, 5, 2353–2370, 2009, DOI: 10.1021/ct900242e ! furanose monosaccharides Hatcher, E. R.; Guvench, O.; MacKerell, Hatcher, E., Guvench, O., and MacKerell, Jr., A.D. “CHARMM Additive All-Atom Force Field for Aldopentofuranose Carbohydrates and Fructofuranose.” Journal of Physical Chemistry B. 113:12466-76, 2009, PMID: 19694450 !CHARMM GENERAL FORCE FIELD, CGenFF Vanommeslaeghe, K., Hatcher, E.,Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I. and Mackerell Jr., A.D., J. Comput. Chem., DOI: 10.1002/jcc.21367