# # 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 0 PARALLEL 0 # PREFIX snapshot PATH ./ START 1 STOP 31 OFFSET 1 # COMPLEX 1 RECEPTOR 1 LIGAND 1 # COMPT ./com.prmtop RECPT ./rec.prmtop LIGPT ./lig.prmtop # GC 0 AS 0 DC 0 # MM 1 GB 1 PB 1 MS 1 # NM 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 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 1.0 EXDI 80.0 SCALE 2 LINIT 1000 ISTRNG 0.0 RADIOPT 0 ARCRES 0.0625 INP 1 # SURFTEN 0.005 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) 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) # IGB 1 GBSA 1 SALTCON 0.00 EXTDIEL 80.0 INTDIEL 1.0 # SURFTEN 0.005 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 0.0 # ################################################################################ @PROGRAMS # # Additional program executables can be defined here # # ################################################################################