24小时热门版块排行榜

返回列表

当前只显示满足指定条件的回帖，点击这里查看本话题的所有回帖

落雁双飞

银虫 (小有名气)

应助: 0 (幼儿园)
金币: 162.9
帖子: 138
在线: 32.2小时
虫号: 791704

[交流] 在计算能量分解时存在的问题，希望大家能共同探讨一下

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

回复此楼