# # Input parameters for mm_pbsa.pl # # Holger Gohlke # 15.02.2012 # ################################################################################ @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 to Ala during generation of snapshots from # trajectories. # DC - Decompose the free energies into individual contributions. # (When using DC, MM and GB must be set to 1, even if a PB decomposition # is also requested.) # # 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 the PB method and # computation 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 either # with the LCPO (GBSA == 1) or the ICOSA (GBSA == 2) method in sander # (see below). # 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 0 # PREFIX 2B.d3. PATH ./ START 3000 STOP 5000 OFFSET 1000 # COMPLEX 1 RECEPTOR 1 LIGAND 1 # COMPT ./2Bcomp.top RECPT ./CFHrec.top LIGPT ./2Blig.top # GC 1 AS 1 DC 0 # MM 1 GB 0 PB 1 MS 0 # NM 0 # ################################################################################ @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 or PB, and nonpolar contributions to # desolvation using the ICOSA 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. # ################################################################################ @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 program is used for solving the PB equation: # Delphi (PROC == 1), PBSA (PROC == 2), or APBS (PROC == 3). # 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. # SCALE - Lattice spacing in no. of grids per Angstrom. # LINIT - No. of iterations with linear PB equation. # 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 with respect to the # reaction field energies computed in the TIP3P explicit solvents # (Tan & Luo, J. Phys. Chem. B, 2006, 110, 18680-18687). # 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). # ARCRES - Resolution (in the unit of Angstrom) of solvent accessible arcs # IVCAP - If set to 1, a solvent sphere (specified by CUTCAP,XCAP,YCAP, # and ZCAP) is excised from a box of water. If set to 5, a solvent # shell is excised, specified by CUTCAP (the thickness of the shell # in A). The electrostatic part of the solvation free energy is # estimated from a linear response approximation using the explicit # solvent plus a reaction field contribution from outside the sphere # (i.e., a hybrid solvation approach is pursued). # In addition, the nonpolar contribution is estimated from a sum of # (attractive) dispersion interactions calc. between the solute and # the solvent molecules plus a (repulsive) cavity contribution # (Gohlke & Case, J. comput. Chem. 2004, 25, 238-250). # For the latter, the surface calculation must be done with MS = 1 and # the PROBE should be set to 1.4 to get the solvent excluded surface. # In this case bondi radii are used as cavity radii set. # CUTCAP - Radius of the water sphere or thickness of the water shell. # Note that the sphere must enclose the whole solute. # XCAP - Location of the center of the water sphere. # YCAP # ZCAP # # NP Parameters for nonpolar solvation energies if MS = 0 # # INP - Option for modeling nonpolar solvation free energy. # See sander PB documentation for more information on the # implementations by Tan and Luo. # 1: uses the solvent-accessible-surface area to correlate total # nonpolar solvation free energy: # Gnp = SURFTEN * SASA + SURFOFF. 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 + SURFTEN * SASA + SURFOFF. # When this option is used, RADIOPT has to be set to 1, # i.e. the radii set optimized by Tan and Luo. # SURFTEN/SURFOFF - Values used to compute the nonpolar # solvation free energy Gnp acccording to INP. # If INP = 1 and RADIOPT = 0 (default, see above), # use SURFTEN/SURFOFF parameters that fit with the radii from the # prmtop file, e.g., # use SURFTEN: 0.00542 and SURFOFF: 0.92 for PARSE radii. # If INP = 2 and RADIOPT = 1, please set these to the following: # SURFTEN: 0.0378; OFFSET: -0.5692 # # NP Parameters for nonpolar solvation energies if MS = 1 # # SURFTEN/SURFOFF - Values used to compute the nonpolar contribution Gnp to # the desolvation according to: # (I) Gnp = SURFTEN * SASA + SURFOFF (if IVCAP == 0) # Use parameters that fit with the radii from the reaction field # calculation. E.g., use SURFTEN: 0.00542, SURFOFF: 0.92 for # PARSE radii # (II) Gnp = Gdisp + Gcavity = Gdisp + SURFTEN * SESA + SURFOFF (IVCAP > 0) # Nonpolar solvation free energy calculated as discribed for IVCAP > 0 # above. In this case use SURFTEN: 0.069; SURFOFF: 0.00 for # calculating the Gcavity contribution. # PROC 2 REFE 0 INDI 3.0 EXDI 80.0 SCALE 2 LINIT 1000 ISTRNG 0.0 RADIOPT 0 ARCRES 0.0625 INP 1 # SURFTEN 0.00542 SURFOFF 0.92 # 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 3.0 # ################################################################################ @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) and 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. # Choose SURFTEN and SURFOFF values according to the selected # GB model, e.g.: # IGB=1 : SURFTEN=0.0072, SURFOFF=0.0, mbondi radii # (Tsui & Case, Biopolymers 2000, 56, 275-291) # IGB=2 : SURFTEN=0.005, SURFOFF=0.0, mbondi2 radii # (Onufriev et al, Proteins 2004, 55, 383-394) # IGB=5 : SURFTEN=0.005, SURFOFF=0.0, mbondi2 radii # (Onufriev et al, Proteins 2004, 55, 383-394) # # ################################################################################ @MS # # Molsurf parameters (this section is only relevant if MS = 1 above) # # PROBE - Radius of the probe sphere used to calculate the SAS. # In general, since Bondi radii are already augmented by 1.4A, # PROBE should be 0.0 # In IVCAP = 1 or 5, the solvent excluded surface is required for # calculating the cavity contribution. Bondi radii are not # augmented in this case and PROBE should be 1.4. # # ################################################################################ @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) # ################################################################################ @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 12414 NSTART 3000 NSTOP 5000 NFREQ 1000 # NUMBER_LIG_GROUPS 3 LSTART 1 LSTOP 3083 LSTART 12403 LSTOP 12403 LSTART 12407 LSTOP 12408 NUMBER_REC_GROUPS 9 RSTART 3084 RSTOP 6180 RSTART 6181 RSTOP 9291 RSTART 9292 RSTOP 12402 RSTART 12404 RSTOP 12404 RSTART 12405 RSTOP 12405 RSTART 12406 RSTOP 12406 RSTART 12409 RSTOP 12410 RSTART 12411 RSTOP 12412 RSTART 12413 RSTOP 12414 # ################################################################################ @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 1 MUTANT_ATOM1 24 MUTANT_ATOM2 0 MUTANT_KEEP 35 MUTANT_REFERENCE 21 # ################################################################################ @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 ../BCFHsolv10ns_noH2O.mdcrd # ################################################################################ @PROGRAMS # # Additional program executables can be defined here # # ################################################################################