CHARMM Emprical Energy Function Parameters This section describes parameters in the CHARMM empirical energy function. * Menu: * Overview:: Overview of CHARMM parameter file by A. D. Mackerell Jr. * 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.
Overview of CHARMM parameter files By Alexander D. MacKerell Jr., July 1997 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) 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 (G) NBFIX H O -0.30 1.50 -0.15 1.50 (H) HBONDs hbond terms (IO.DOC) H O -0.00 1.00 (I) 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. 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) may be used. 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. By convention, the first atom of an improper dihedral (type A-X-X-B or A-B-C-D) is usually the central atom. This had been a general rule in the past. Parameters for (F) 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 (G) 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 (H) contains the hydogen bond well depths and minimum radii for various atom pairs. In current versions of the CHARMM parameter sets (PARAM19, CHARMM22 protein and nucleic acid 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.
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 CHARMM22 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.
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 CHARMM22. 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 CHARMM). A test should be performed on a (deoxy)ribose containing 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 CHARMM). A test should be performed on a (deoxy)ribose containing 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.
(A) Topology files (1) top_all22_prot.inp all hydrogen RTF for proteins (2) top_all22_model.inp all hydrogen RTF for protein model cmpds (3) top_all22_sugar.rtf all hydrogen RTF for sugars (4) top_all27_na.rtf all hydrogen RTF for nucleic acids (5) top_all27_lipid.rtf all hydrogen RTF for lipids (6) top_all27_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids (7) top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids (9) top_all27_prot_lipid.rtf all hydrogen RTF for proteins and lipids (9) toph19.inp extended atom RTF for proteins (10) toprna10r_22.inp extended atom RTF for nucleic acids (B) Parameter files (1) par_all22_prot.inp all hydrogen parameters for proteins (2) par_all22_sugar.rtf all hydrogen parameters for sugars (3) par_all27_na.rtf all hydrogen parameters for nucleic acids (4) par_all27_lipid.rtf all hydrogen parameters for lipids (5) par_all27_na_lipid.rtf all hydrogen parameters for nucleic acids and lipids (6) par_all27_prot_na.rtf all hydrogen parameters for proteins and nucleic acids (7) par_all27_prot_lipid.rtf all hydrogen parameters for proteins and lipids (8) param19.inp extended atom parameters for proteins (9) pardna10_22.inp extended atom parameters for nucleic acids (10) 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. 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 firstname.lastname@example.org. ADM Jr., August 1999 http://www.pharmacy.ab.umd.edu/~alex/ References 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. 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 CHARMM22 PROTEIN PARAMETERS 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. 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 CHARMM27 NUCLEIC ACID PARAMETERS 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. Journal of Computational Chemsitry, 2000, 21:86-104. and 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. Journal of Computational Chemsitry, 2000, 21:105-120. CHARMM27 LIPID PARAMETERS Feller, S. and MacKerell, Jr., A.D. manuscript in preparation. 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. CHARMM22 NUCLEIC ACID PARAMETERS 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. CHARMM22 LIPID PARAMETERS Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M. Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and Applications, in "Biological Membranes: A Molecular Perspective from Computation and Experiment," K.M. Merz and B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81. FOR ALKENES Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D., Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration: Parametrization and Comparison with Diffraction Studies. Biophysical Journal 1997, 73: 2269-2279.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute