[gmx-users] atom numbering

[Justin Lemkul]

On 12/1/15 7:38 AM, Marta Wisniewska wrote:
> Dear Gromacs users,
>
> My problem focus on number order. I am preparing my system to md. In my pdb
> file I made a some modifications (delete chains or ligand compounds).
> During preparation of topology and gro file, the residue number ordering is
> changed. Is there any possibility to preserve number ordering from pdb file
> during pdb2gmx transfer?
>

Use the -norenum 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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