[gmx-users] request

Justin Lemkul jalemkul at vt.edu
Tue Apr 16 15:51:29 CEST 2013

On 4/16/13 9:07 AM, Group Gro wrote:
> Dear GROMACS users,
> Hi.
> I want to study different protein-drug complexes and I follow the procedure mentioned in the http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/. I copied and pasted the positions of each drug to the end of conf.gro and did other steps. Is this approach true while I don't know the best place to dock it?If not, how can I add drug without using Autodock, Gold, or other docking softwares? Doeas each drug find the best place to dock?

The approach of copying and pasting coordinates assumes you believe that those 
coordinates are a realistic representation (i.e. from docking or 
crystallography).  If you just place the molecule in some random way, there's no 
telling if it's right.  The starting position will heavily bias the outcome.  If 
you're not sure, invest some time in learning docking.

> My next question is this: When I have different drugs and consider each complex of them separately, what factor(s) should be my criteria to find the best drug which has the highest effect on the protein (each drug has different nubmer of atoms)?

I would suggest you consult the literature here and make an assessment based on 
what you know about your particular protein.  There is no catch-all answer. 
Binding free energy may be useful, but that's just a generic answer with no 
knowledge of what you're trying to do.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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