On 7/4/13 3:16 PM, Sainitin Donakonda wrote:
Hi Justin,
Thanks for reply.
using pdbgmx i generated charmm27 force field for protein
I prepared ligand topologies using swissparam online tool for all 5
ligands. But it worked for 4 and 5th one is creating problem at energy
minimization step.
And how about the other question I asked - the source of the initial
configurations? How good are the topologies? What does visual inspection of
the EM trajectory show you? The steps listed on
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
still apply, regardless of whether you're doing EM or MD.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Associate
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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