Dear all
I am performing mmpbsa calculation for DNA-ligand (amber 10). I face whit
two problem through running and analyzing:
1. when running mm_pbsa.pl, this massage is appeared:
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
after termination, and get the snapshot_statistics.out, I check the
snapshot_com.all.out,
no massages or strange word is observed. By watching binding_energy.log file,
this warning is written in it:
Reading snapshot_rec.all.out
Checking consistency of CALC
Checking consistency of DATA
Entry 1 NM SROT 0 exists -> overwriting
Entry 1 NM SROT 1 exists -> overwriting
Should I concern or ignore this warning? and how can I fix it?
2. Energy decomposition in snapshot_statistics.out shows unreliable data such
as:
VDW energy is positive, and INT energy is not zero?
system consists of DNA, ligand and Na+ ions. Simulation is done in explicit
solvent for 5 ns.
here is my binding_energy.mmpbsa file:
#
# 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 400
STOP 500
OFFSET 1
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./dna-ox.prmtop
RECPT ./dna.prmtop
LIGPT ./lig.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 1
#
################################################################################
.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 5
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
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 2
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
#
################################################################################
.NM
#
# Parameters for sander/nmode calculation (this section is only relevant if
NM = 1 above)
#
# The following parameters are passed to sander (for minimization) and
nmode
# (for entropy calculation using gasphase statistical mechanics).
# For further details see documentation.
#
# DIELC - (Distance-dependent) dielectric constant
# MAXCYC - Maximum number of cycles of minimization.
# DRMS - Convergence criterion for the energy gradient.
#
DIELC 4
MAXCYC 1000
DRMS 0.1
#
################################################################################
.PROGRAMS
#
# Additional program executables can be defined here
#
################################################################################
Any help is appreciated.
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Received on Mon Nov 17 2014 - 00:30:02 PST
