# # Input parameters for mm_pbsa.pl # # Holger Gohlke # 08.01.2002 ################################################################################ @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). # # 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. # # 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 NPOPT 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 NPOPT option in pbsa (see below). # NM - Calculation of entropies with nmode. # VERBOSE 0 PREFIX snap PATH ./snaps #START 1 #STOP 10 #OFFSET 1 # COMPLEX 1 RECEPTOR 1 LIGAND 1 # COMPT ./complex.prmtop RECPT ./rsl.prmtop LIGPT ./lig.prmtop # GC 1 AS 0 DC 0 # MM 0 GB 0 PB 0 MS 0 # NM 1 ################################################################################## @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 # trajectory files; "NO" means opposite. # NTOTAL - Total number of atoms per snapshot printed in the trajectory file # (including water, ions, ...). # NSTART - Start structure extraction from the NSTART-th snapshot. # NSTOP - Stop structure extraction at the NSTOP-th 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 YES NTOTAL 30885 NSTART 1 NSTOP 10 NFREQ 1 # NUMBER_LIG_GROUPS 1 LSTART 3923 LSTOP 3948 NUMBER_REC_GROUPS 1 RSTART 1 RSTOP 3922 # ################################################################################### @TRAJECTORY # # Trajectory names # # The following trajectories are used to extract snapshots with "make_crd_hg": # Each trajectory name must be preceded 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 ./prod.mdcrd # # # # ################################################################################ @DECOMP # # Energy decomposition parameters (this section is only relevant if DC = 1 above) # # Energy decomposition is performed for gasphase energies, desolvation free # energies calculated with GB, and nonpolar contributions to desolvation # using the LCPO method. # For amino acids, decomposition is also performed with respect to backbone # and sidechain atoms. # # DCTYPE - Values of 1 or 2 yield a decomposition on a per-residue basis, # values of 3 or 4 yield a decomposition on a pairwise per-residue # basis. For the latter, so far the number of pairs must not # exceed the number of residues in the molecule considered. # Values 1 or 3 add 1-4 interactions to bond contributions. # Values 2 or 4 add 1-4 interactions to either electrostatic or vdW # contributions. # # COMREC - Residues belonging to the receptor molecule IN THE COMPLEX. # COMLIG - Residues belonging to the ligand molecule IN THE COMPLEX. # RECRES - Residues in the receptor molecule. # LIGRES - Residues in the ligand molecule. # {COM,REC,LIG}PRI - Residues considered for output. # {REC,LIG}MAP - Residues in the complex which are equivalent to the residues # in the receptor molecule or the ligand molecule. # DCTYPE 2 # COMREC 1-266 COMLIG 267-268 COMPRI 1-266 RECRES 1-266 RECPRI 1-266 RECMAP 1-266 LIGRES 1-2 LIGPRI 1-2 LIGMAP 267-268 ################################################################################ @PB # # PB parameters (this section is only relevant if PB = 1 above) # # The following parameters are passed to the PB solver. # Additional input parameters may also be added here. See the sander PB # documentation for more options. # # PROC - Determines which method is used for solving the PB equation: # By default, PROC = 2, the pbsa program of the AMBER suite is used. # REFE - Determines which reference state is taken for PB calc: # By default, REFE = 0, reaction field energy is calculated with # EXDI/INDI. Here, INDI must agree with DIELC from MM part. # INDI - Dielectric constant for the solute. # EXDI - Dielectric constant for the surrounding solvent. # ISTRNG - Ionic strength (in mM) for the Poisson-Boltzmann solvent. # PRBRAD - Solvent probe radius in Angstrom: # 1.4: with the radii in the prmtop files. Default. # 1.6: with the radii optimized by Tan and Luo (In preparation). # See RADIOPT on how to choose a cavity radii set. # RADIOPT - Option to set up radii for PB calc: # 0: uses the radii from the prmtop file. Default. # 1: uses the radii optimized by Tan and Luo (In preparation) # with respect to the reaction field energies computed # in the TIP3P explicit solvents. Note that optimized radii # are based on AMBER atom types (upper case) and charges. # Radii from the prmtop files are used if the atom types # are defined by antechamber (lower case). # SCALE - Lattice spacing in no. of grids per Angstrom. # LINIT - No. of iterations with linear PB equation. # # NP Parameters for nonpolar solvation energies if MS = 0 # # NPOPT - Option for modeling nonpolar solvation free energy. # See sander PB documentation for more information on the # implementations by Tan and Luo (In preparation). # 1: uses the solvent-accessible-surface area to correlate total # nonpolar solvation free energy: # Gnp = CAVITY_SURFTEN * SASA + CAVITY_OFFSET. Default. # 2: uses the solvent-accessible-surface area to correlate the # repulsive (cavity) term only, and uses a surface-integration # approach to compute the attractive (dispersion) term: # Gnp = Gdisp + Gcavity # = Gdisp + CAVITY_SURFTEN * SASA + CAVITY_OFFSET. # When this option is used, RADIOPT has to be set to 1, # i.e. the radii set optimized by Tan and Luo to mimic Gnp # in TIP3P explicit solvents. Otherwise, there is no guarantee # that Gnp matches that in explicit solvents. # CAVITY_SURFTEN/CAVITY_OFFSET - Values used to compute the nonpolar # solvation free energy Gnp according NPOPT. The default values # are for NPOPT set to 0 and RADIOPT set to 0 (see above). # If NPOPT is set to 1 and RADIOPT set to 1, these two lines # can be removed, i.e. use the default values set in pbsa # for this nonpolar solvation model. Otherwise, please # set these to the following: # CAVITY_SURFTEN: 0.04356 # CAVITY_OFFSET: -1.008 # # NP Parameters for nonpolar solvation energies if MS = 1 # # SURFTEN/SURFOFF - Values used to compute the nonpolar contribution Gnp to # the desolvation according to Gnp = SURFTEN * SASA + SURFOFF. # PROC 2 REFE 0 INDI 1.0 EXDI 80.0 SCALE 2 LINIT 1000 PRBRAD 1.4 ISTRNG 0.0 RADIOPT 0 NPOPT 1 CAVITY_SURFTEN 0.0072 CAVITY_OFFSET 0.00 # SURFTEN 0.0072 SURFOFF 0.00 # IVCAP 0 CUTCAP -1.0 XCAP 0.0 YCAP 0.0 ZCAP 0.0 # ################################################################################ @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 # ################################################################################ @GB # # GB parameters (this section is only relevant if GB = 1 above) # # The first group of the following parameters are passed to sander. # For further details see the sander documentation. # # IGB - Switches between Tsui's GB (1), Onufriev's GB (2, 5). # GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc. # Decomposition only works with ICOSA. # SALTCON - Concentration (in M) of 1-1 mobile counterions in solution. # EXTDIEL - Dielectricity constant for the solvent. # INTDIEL - Dielectricity constant for the solute # # SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp to # the desolvation according to Gnp = SURFTEN * SASA + SURFOFF. # IGB 2 GBSA 1 SALTCON 0.00 EXTDIEL 80.0 INTDIEL 1.0 # SURFTEN 0.0072 SURFOFF 0.00 # ################################################################################ @MS # Molsurf parameters (this section is only relevant if MS = 1 above) # # PROBE - Radius of the probe sphere used to calculate the SAS. # Since Bondi radii are already augmented by 1.4A, PROBE should be 0.0 # PROBE 0.0 # ################################################################################# @NM # Parameters for sander/nmode calculation (this section is only relevant # if NM = 1 above) # # The following parameters are passed to sander (for minimization) and nmode # (for entropy calculation using gasphase statistical mechanics). # For further details see documentation. # # DIELC - (Distance-dependent) dielectric constant # MAXCYC - Maximum number of cycles of minimization. # DRMS - Convergence criterion for the energy gradient. # DIELC 4 MAXCYC 50000 DRMS 0.001 ################################################################################# @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 # 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 and VAL. # 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 1 MUTANT_ATOM1 229 MUTANT_ATOM2 0 MUTANT_KEEP 244 MUTANT_REFERENCE 226 #MUTANT_ATOM2 1498 #MUTANT_ATOM1 1494 #MUTANT_KEEP 1500 #MUTANT_REFERENCE 1492 #MUTANT_ATOM1 1552 #MUTANT_ATOM2 0 #MUTANT_KEEP 1562 #MUTANT_REFERENCE 1549 # # # ################################################################################# @PROGRAMS # # Additional program executables can be defined here # # ################################################################################