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在计算能量分解时存在的问题，希望大家能共同探讨一下
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我用软件是amber10 这是报错信息： [amber@localhost binding-famo]$ mm_pbsa.pl binding.in > binding.out /usr/local/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c ../snapshot/complex_com.crd.1 -p ../com.prmtop not successful 输出文件如下： =>> Init data Presuming executables of amber suite to be in /usr/local/amber10/exe =>> Reading input parameters Found PREFIX => complex Found PATH => ../snapshot/ Found COMPLEX => 1 Found RECEPTOR => 1 Found LIGAND => 1 Found COMPT => ../com.prmtop Found RECPT => ../rec.prmtop Found LIGPT => ../lig.prmtop Found GC => 0 Found AS => 0 Found DC => 0 Found MM => 1 Found GB => 1 Found PB => 1 Found MS => 1 Found NM => 0 Found PROC => 2 Found REFE => 0 Found INDI => 1.0 Found EXDI => 80.0 Found SCALE => 2 Found LINIT => 1000 Found PRBRAD => 1.4 Found ISTRNG => 0.0 Found RADIOPT => 0 Found NPOPT => 1 Found CAVITY_SURFTEN => 0.0072 Found CAVITY_OFFSET => 0.00 Found SURFTEN => 0.0072 Found SURFOFF => 0.00 Found DIELC => 1.0 Found IGB => 2 Found GBSA => 1 Found SALTCON => 0.00 Found EXTDIEL => 80.0 Found INTDIEL => 1.0 Found SURFTEN => 0.0072 Found SURFOFF => 0.00 Found PROBE => 0.0 =>> Checking sanity Checking GENERAL Setting START to default 1 Setting STOP to default 10e10 Setting OFFSET to default 1 Setting VERBOSE to default 0 Checking MM Checking PB Checking GB Checking MS =>> Creating input Sander input PBSA input =>> Calculating energy / entropy contributions Calc contrib for ../snapshot/complex_com.crd.1 Calc MM/GB/SAS 结合能计算的脚本如下： 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. # PREFIX complex PATH ../snapshot/ # 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 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 # ################################################################################ @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 # ################################################################################# @PROGRAMS # # Additional program executables can be defined here |
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