[gmx-users] coordinates obtained from the Automated Topology Builder

[Justin Lemkul]

On 1/13/14, 12:15 AM, Zalikha Ibrahim wrote:
> Dear GMX Users and Justin,
>
> I am also experienced the same situation as posted above.
> Is that mean I have to introduce the ligand using original coordinates and
> use the topology (.itp) generated from ATB?
>

Yes.  Any external server or program that alters the coordinates of the ligand 
in the absence of its cognate receptor will lead to problems in the simulation.

-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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