Dear Amber Users,
I am trying to do a pairwise energy decomposition with amber9 using mmpbsa.pl.
I get the decomposed pairwise energy value as ******** for some pairs. Can you
please comment on this problem. Is it some error in the calculation. I am also
pasting my decomposition script below.
decomp.in
PREFIX mad
PATH ./
#
COMPLEX 1
RECEPTOR 0
LIGAND 0
#
COMPT mad.prmtop
RECPT XXX
LIGPT XXX
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 0
MS 0
#
NM 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 4
#
COMREC 1-1577
COMLIG 1576-1577
COMPRI 1-1577
RECRES 1-1575
RECPRI 1-1575
RECMAP 1-1575
LIGRES 1576-1577
LIGPRI 1576-1577
LIGMAP 1576-1577
#
################################################################################
.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 0.0072
SURFOFF 0.00
#
################################################################################
.PROGRAMS
#
# Program executables
#
DELPHI /home/gohlke/src/delphi.98/exe/delphi
################################################################################
Thanks a lot in advance.
Regards,
Moitrayee
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Received on Mon Aug 22 2011 - 06:30:03 PDT
