[gmx-users] forming disulfide linkage between two chains

[Justin Lemkul]

On 8/5/15 3:52 AM, tasneem kausar wrote:
> sir
>
> I am trying to make disulfide linkage between chain A and B.
> The command line is "pdb2gmx -f prtn.pdb -o prtn.gro -p prtn.top -ss.
> I have used -ss option of pdb2gmx but disufide linkage is not formed
> between the chains A and B.
> What is the possible way to form the disulfide linkage in Gromacs usind the
> pdb2gmx.

You need to use the -merge option.

-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 629
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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