# # 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 0 PARALLEL 0 # PREFIX Lig_5 PATH . START 1 STOP 3 OFFSET 1 # COMPLEX 0 RECEPTOR 1 LIGAND 0 # COMPT XXX RECPT Lig_5_gb0_pb2_solv_lig.top LIGPT XXX # GC 0 AS 0 DC 0 # MM 0 GB 0 PB 1 MS 1 # 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, 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. # DCTYPE 0 # COMREC 0 COMLIG 0 COMPRI 0 RECRES 0 RECPRI 0 RECMAP 0 LIGRES 1-1 LIGPRI 1-1 LIGMAP 0 ################################################################################ @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. # 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 water 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. 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. # 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 (In preparation). # 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 to mimic Gnp # in TIP3P explicit solvents. Otherwise, there is no guarantee # that Gnp matches that in explicit solvents. # 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; SURFOFF: 0.92 for PARSE radii. # If INP = 2 and RADIOPT = 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: # SURFTEN: 0.04356; 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 either # (I) Gnp = SURFTEN * SASA + SURFOFF (if IVCAP = 0) or # (II) Gnp = Gdisp + Gcavity = Gdisp + SURFTEN * SESA + SURFOFF (if IVCAP > 0). # In the case of (I), use parameters that fit with the radii from the # reaction field calculation. E.g., use SURFTEN: 0.00542, SURFOFF: 0.92 # for PARSE radii or use SURFTEN: 0.005, SURFOFF: 0.86 for Tan & Luo radii. # In the case of (II), use SURFTEN: 0.069; SURFOFF: 0.00 for calculating the # Gcavity contribution. # PROC 2 REFE 0 INDI 1.0 EXDI 80.0 SCALE 2 LINIT 1000 PRBRAD 1.6 ISTRNG 0.0 RADIOPT 1 INP 1 ARCRES 0.0625 # SURFTEN 0.069 SURFOFF 0.0 # IVCAP 5 CUTCAP 15.0 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) 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. # IGB 1 GBSA 0 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. # 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. # PROBE 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) # PROC 1 # MAXCYC 1000 DRMS 0.5 # IGB 1 SALTCON 0.00 EXTDIEL 80.0 SURFTEN 0.0072 # DIELC 4 # ################################################################################ @PROGRAMS # # Additional program executables can be defined here /apps/prod/amber11/exe/sander # # ################################################################################