# # Input parameters for mm_pbsa.pl # # Holger Gohlke # 25.02.2010 # ################################################################################ @GENERAL # # General parameters # 0: means NO; >0: means YES # # mm_pbsa allows to calculate (absolute) free energies for one molecular # species or a free energy difference according to: # # Receptor + Ligand = Complex, # DeltaG = G(Complex) - G(Receptor) - G(Ligand). # # VERBOSE - If set to 1, input and output files are not removed. This is useful for # debugging purposes. # PARALLEL - If set to values > 1, energy calculations for snapshots are done # in parallel, using PARALLEL number of threads. # # PREFIX - To the prefix, "{_com, _rec, _lig}.crd.Number" is added during # generation of snapshots as well as during mm_pbsa calculations. # PATH - Specifies the location where to store or get snapshots. # START - Specifies the first snapshot to be used in energy calculations (optional, defaults to 1). # STOP - Specifies the last snapshot to be used in energy calculations (optional, defaults to 10e10). # OFFSET - Specifies the offset between snapshots in energy calculations (optional, defaults to 1). # # COMPLEX - Set to 1 if free energy difference is calculated. # RECEPTOR - Set to 1 if either (absolute) free energy or free energy # difference are calculated. # LIGAND - Set to 1 if free energy difference is calculated. # # COMPT - parmtop file for the complex (not necessary for option GC). # RECPT - parmtop file for the receptor (not necessary for option GC). # LIGPT - parmtop file for the ligand (not necessary for option GC). # # GC - Snapshots are generated from trajectories (see below). # AS - Residues are mutated during generation of snapshots from trajectories. # DC - Decompose the free energies into individual contributions # (only works with MM and GB). # # MM - Calculation of gas phase energies using sander. # GB - Calculation of desolvation free energies using the GB models in sander # (see below). # PB - Calculation of desolvation free energies using delphi (see below). # Calculation of nonpolar solvation free energies according to # the INP option in pbsa (see below). # MS - Calculation of nonpolar contributions to desolvation using molsurf # (see below). # If MS == 0 and GB == 1, nonpolar contributions are calculated with the # LCPO method in sander. # If MS == 0 and PB == 1, nonpolar contributions are calculated according # the INP option in pbsa (see below). # NM - Calculation of entropies with nmode. # VERBOSE 1 PARALLEL 2 # PREFIX test PATH ./output/ START 1 STOP 3 OFFSET 1 # COMPLEX 1 RECEPTOR 1 LIGAND 1 # COMPT ./complex.prmtop RECPT ./receptor.prmtop LIGPT ./ligand.prmtop # GC 1 AS 0 DC 0 # MM 1 GB 0 PB 0 MS 0 # NM 1 # ################################################################################# @NM # # Parameters for sander/nmode calculation (this section is only relevant if NM = 1 above) # # The following parameters are used for entropy calculation using # gasphase statistical mechanics. # For further details see documentation. # # PROC - Determines which method is used for the calculations: # By default, PROC = 1, the NAB implementation of nmode is used. # This allows using either a GB model or a distance-dependent dielectric # for electrostatic energies. No entropy decomposition is possible, however. # If PROC = 2, the "original" nmode implementation is used. # Here, only a distance-dependent dielectric is avaliable for # electrostatic energies. Entropy decomposition is possible here, too. # MAXCYC - Maximum number of cycles of minimization. # DRMS - Convergence criterion for the energy gradient. # IGB - Switches between no GB (i.e., vacuum electrostatics) (0) or Tsui's GB (1). # SALTCON - Concentration (in M) of 1-1 mobile counterions in solution. # EXTDIEL - Dielectricity constant for the solvent. # SURFTEN - Value used to compute the nonpolar contribution Gnp to # the desolvation according to Gnp = SURFTEN * SASA. # DIELC - (Distance-dependent) dielectric constant (if IGB = 0) # PROC 1 # MAXCYC 10000 DRMS 0.5 # IGB 1 SALTCON 0.00 EXTDIEL 80.0 SURFTEN 0.0072 # DIELC 4 # ################################################################################ @MAKECRD # # The following parameters are passed to make_crd_hg, which extracts snapshots # from trajectory files. (This section is only relevant if GC = 1 OR AS = 1 above.) # # BOX - "YES" means that periodic boundary conditions were used during MD # simulation and that box information has been printed in the # trajecotry files; "NO" means opposite. # NTOTAL - Total number of atoms per snapshot printed in the trajectory file # (including water, ions, ...). # NSTART - Start structure extraction from NSTART snapshot. # NSTOP - Stop structure extraction at NSTOP snapshot. # NFREQ - Every NFREQ structure will be extracted from the trajectory. # # NUMBER_LIG_GROUPS - Number of subsequent LSTART/LSTOP combinations to # extract atoms belonging to the ligand. # LSTART - Number of first ligand atom in the trajectory entry. # LSTOP - Number of last ligand atom in the trajectory entry. # NUMBER_REC_GROUPS - Number of subsequent RSTART/RSTOP combinations to # extract atoms belonging to the receptor. # RSTART - Number of first receptor atom in the trajectory entry. # RSTOP - Number of last receptor atom in the trajectory entry. # Note: If only one molecular species is extracted, use only the receptor # parameters (NUMBER_REC_GROUPS, RSTART, RSTOP). # BOX NO NTOTAL 1233 NSTART 1 NSTOP 3 NFREQ 1 # NUMBER_REC_GROUPS 1 RSTART 1084 RSTOP 1233 NUMBER_LIG_GROUPS 1 LSTART 1 LSTOP 1083 # ################################################################################# @ALASCAN # # The following parameters are additionally passed to make_crd_hg in conjunction # with the ones from the @MAKECRD section if "alanine scanning" is requested. # (This section is only relevant if AS = 1 above.) # # The description of the parameters is taken from Irina Massova. # # NUMBER_MUTANT_GROUPS - Total number of mutated residues. For each mutated # residue, the following four parameters must be given # subsequently. # MUTANT_ATOM1 - If residue is mutated to Ala then this is a pointer on CG # atom of the mutated residue for all residues except Thr, # Ile and Val. # A pointer to CG2 if Thr, Ile or Val residue is mutated to Ala # A pointer to OG if Ser residue is mutated to Ala # If residue is mutated to Gly then this is a pointer on CB. # MUTANT_ATOM2 - If residue is mutated to Ala then this should be zero for # all mutated residues except Thr, VAL, and ILE. # A pointer on OG1 if Thr residue is mutated to Ala. # A pointer on CG1 if VAL or ILE residue is mutated to Ala. # If residue is mutated to Gly then this should be always zero. # MUTANT_KEEP - A pointer on C atom (carbonyl atom) for the mutated residue. # MUTANT_REFERENCE - If residue is mutated to Ala then this is a pointer on # CB atom for the mutated residue. # If residue is mutated to Gly then this is a pointer on # CA atom for the mutated residue. # Note: The method will not work for a smaller residue mutation to a bigger # for example Gly -> Ala mutation. # Note: Maximum number of the simultaneously mutated residues is 40. # NUMBER_MUTANT_GROUPS 3 MUTANT_ATOM1 1480 MUTANT_ATOM2 0 MUTANT_KEEP 1486 MUTANT_REFERENCE 1477 MUTANT_ATOM2 1498 MUTANT_ATOM1 1494 MUTANT_KEEP 1500 MUTANT_REFERENCE 1492 MUTANT_ATOM1 1552 MUTANT_ATOM2 0 MUTANT_KEEP 1562 MUTANT_REFERENCE 1549 # ################################################################################# @MM # # MM parameters (this section is only relevant if MM = 1 above) # # The following parameters are passed to sander. # For further details see the sander documentation. # # DIELC - Dielectricity constant for electrostatic interactions. # Note: This is not related to GB calculations. # DIELC 1.0 # ################################################################################ @TRAJECTORY # # Trajectory names # # The following trajectories are used to extract snapshots with "make_crd_hg": # Each trajectory name must be preceeded by the TRAJECTORY card. # Subsequent trajectories are considered together; trajectories may be # in ascii as well as in .gz format. # To be able to identify the title line, it must be identical in all files. # TRAJECTORY ./md.mdcrd # @PROGRAMS # # Additional program executables can be defined here # # ###############################################################################