[gmx-users] Fwd: Need Help in Gromacs

[Justin Lemkul]

On 3/5/14, 6:21 AM, Balasubramani GL wrote:
>
>
> -------- Original Message --------
>
> 		SUBJECT:
>   		Need Help in Gromacs
>
> 		DATE:
>   		2014-03-05 16:47
>
> 		FROM:
>   		Balasubramani GL <glbala87 at imtech.res.in>
>
> 		TO:
>   		drbevan at vt.edu
>
> Dear all,
>
>   We are simulating a few protein-ligand complexes by gromacs. For
> parameter generation of non protein ligands we used prodrg server and
> gromacs46a1 force field. We performed the PCA analysis. But strangely
> the ligands are completely out of the protein molecule. Kindly suggest
> some measures to treat this problem.
>

Before or after PCA?  If it's before, it's likely a PBC issue, but the ligand 
could dissociate if its topology is bad.

> Additionally we found that the in the tutorial mentioned on
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
> for protein ligand the tutors have reassigned the charges and other
> paramers for th ligand used in this tutorial following a paper below:
>
> PRACTICAL CONSIDERATIONS FOR BUILDING GROMOS-COMPATIBLE SMALL-MOLECULE
> TOPOLOGIES
>
> I request you to kindly send me a pdf copy of this paper. Also i will be
> grateful to you if you can suggest something to solve the above
> explained problem.
>

Contact me off-list and I will get you a copy of the paper.  I cannot post the 
paper to the list or provide the direct access link here as it would be a 
violation of the copyright policy.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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
http://mackerell.umaryland.edu/~jalemkul

==================================================