[gmx-users] Issue in Energy minimization protein-ligand complex

[Justin Lemkul]

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

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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