Hi,
I am trying to perform per residue binding energy decomposition on a
protein-ligand complex by using Amber MMPBSA.pl script to find out the
differences in energies of each residue in both apo and holo systems.
The generated output is a large file containing the following information:
Number Residue SINT BINT
TINT SVDW BVDW TVDW
SELE BELE TELE
SGAS BGAS TGAS SGB
BGB TGB SGBSUR
BGBSUR TGBSUR SGBSOL
BGBSOL TGBSOL SGBTOT
BGBTOT TGBTOT
It is difficult to understand the output of "snapshot_statistics.out" file.
There is an option in mmpbsa.py to add dec_verbose to the input file in
order to reduce/increase the details in the out file as follows:
dec_verbose:
Set the level of output to print in the decomp_output file.
0: DELTA energy, total contribution only.
1: DELTA energy, total, sidechain, and backbone contributions.
2: Complex, Receptor, Ligand, and DELTA energies, total contribution only.
3: Complex,Receptor, Ligand, and DELTA energies, total, sidechain, and
backbone contributions (all data) (Default 0)
Is there any way to add verbose in perl script to get the Complex,
Receptor, Ligand, and DELTA energies, for total contribution only?
Secondly, can these results be interpreted as plots of binding energies
versus residues?
Any information you can provide me would be greatly appreciated.
Many Thanks
Following is the input file:
Sample mm_pbsa.in3 file for MM/GBSA decomposotion. #
# Input parameters for mm_pbsa.pl
# This example just generates snapshots from a trajectory file
#
# 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).
# MS - Calculation of nonpolar contributions to desolvation using molsurf
# (see below).
# If MS == 0, nonpolar contributions are calculated with the LCPO
method
# in sander.
# NM - Calculation of entropies with nmode.
#
PREFIX btn1
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT compl.prmtop
RECPT prot.prmtop
LIGPT lig.prmtop
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 0
MS 0
#
NM 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), 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 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.00542
SURFOFF 0.92
#
################################################################################
.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
#
#
################################################################################
.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 LCPO 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 2
#
COMREC 1-497
COMLIG 498-498
COMPRI 1-498
RECRES 1-497
RECPRI 1-497
RECMAP 1-497
LIGRES 1-1
LIGPRI 1-1
LIGMAP 498-498
#
#
################################################################################
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Received on Fri Jul 13 2018 - 10:00:02 PDT
