[gmx-users] LIGAND TOPOLOGY

[Justin Lemkul]

On 8/27/13 5:10 AM, MUSYOKA THOMMAS wrote:
> Dear users,
> I have been trying to build la ligand topology of my ligand through the
> PRODRG web server.
> I have the following queries;
> According to Justin's important tutorial (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
> i am lost on how to allocate equivalent charges to equivalent groups. I
> have read the recommended paper but seems still i have issues in allocating
> the correct charges to my groups.
>

You'll have to be a lot more specific with what you're dealing with and what 
you're doing if you want to get any useful help.

> Secondly, its about how to determine which groups are encompassed by a
> charge group
>
> Attached find in my PRODRG input file.

Attachments are not allowed on the mailing list.

> Someone out there help me in understanding this.

Charge groups are used in the Gromos96 force fields and typically contain 2-4 
atoms such that the group has an integral charge (generally -1, 0, or 1). 
Figures 1, 3, 4, and 5 of our paper (dx.doi.org/10.1021/ci100335w) show how to 
properly assign charge groups in molecules of increasing complexity.  Our work 
should have encompassed almost all of the most commonly encountered functional 
groups.  Other examples for well-known molecules can be found in the .rtp file 
for the force field.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
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

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