[gmx-users] PRODRG

[Justin Lemkul]

On 5/26/14, 1:00 PM, Negar Parvizi wrote:
> Dear all users,
>
> I am using Protein-Ligand Complex tutorial (Justin Lemkul tutorial). For making .pdb file of ligand, we should use PRODRG(draw molecule with JME Editor).
>   Here is my question that when i draw my ligand in JME Editor, which conformer should i select ? because different conformer gives different PRODRG output files.
>

If you are dealing with a protein-ligand complex, don't you already have 
coordinates for the ligand?  In that case, the JME editor is not even necessary.

Beware PRODRG topologies; they are generally not suitable for MD.

-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

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