[gmx-users] New Molecule Topology

[Justin Lemkul]

On 5/28/14, 1:33 PM, Todor Antonijevic wrote:
> Hi,
>
> I would like to create a topology file for cholesteryl oleate molecule.
> Is it a good practice to use PRODRG server to generate all connections, and
> then to change atom types and parameters according to the Berger force
> field?
>
> Is there a better approach?
>

No matter how you produce the initial topology (PRODRG, ATB, etc), you'll likely 
end up gutting nearly the entire topology to replace the atom types, charges, 
and bonded parameters.

-Justin

-- 
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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

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