Dear AMBER users,
I am keen to do a stability analysis of
various G quadruplex polymorphs using the mm_pbsa.pl available within
AmberTools. My system consists of 716 atoms which includes two potassium
cations. I am using the following input file for the analysis :
.GENERAL
PREFIX test
PATH ./
#
COMPLEX 0
RECEPTOR 1
LIGAND 0
#
RECPT with_ions.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
#
.MM
DIELC 1.0
.GB
IGB 1
GBSA 1
SALTCON 0.2
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.0
#
I am keen to know whether I am doing it right. Unfortunately I could not
make use of the MMPBSA.py script because everytime it complains that the
ligand and the complex topology files are missing. Also since I am using
explicit K+ ions for this analysis do I need to make any changes to the
original script. I would be grateful to know if someone in the community
has done similar analysis using MMPBSA ?
Best,
Debayan Chakraborty
Department of Chemistry,
University of Cambridge
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Received on Sat May 18 2013 - 11:00:02 PDT
