Dear Amber users,
I am getting the following error when running pairwise residuewise decomposition
using mm-pbsa.
Missing values for MM BGAS
I am also attaching the relevant pdb file. I have tried what was suggested in
the previous posts regarding LIGRES/LIGPRI but still getting the error.
Any suggestions will be of immense help.
I am pasting below the input for pairwise residuewise decomposition using mm-pbsa.
PREFIX 2zni
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT comp.prm.top
RECPT rec.prm.top
LIGPT lig.prm.top
#
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 1-278 280-629 631-702
COMLIG 279-279 630-630
COMPRI 1-702
RECRES 1-278 280-629 631-702
RECPRI 1-278 280-629 631-702
RECMAP 1-278 280-629 631-702
LIGRES 1-2
LIGPRI 1-2
LIGMAP 279-279 630-630
#
################################################################################
.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 and Regards,
Moitrayee
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- application/octet-stream attachment: c.pdb
Received on Wed Mar 24 2010 - 12:30:04 PDT
