[gmx-users] atom labeling in forcefield file and pdb are different

[Justin Lemkul]

On 4/4/14, 4:46 AM, Sanchaita wrote:
> Hi, I am trying to perform the simulations of a particular protein having
> NADH as a cofactor.  However, when I try to run pdb2gmx command it
> shows an error. It seems that the gromos96 43a2 force field has parameters
> for NADH but the labeling do not match the labeling done in the pdb file.
> What do I do? Please help.
>

Rename the atoms in the coordinate file to match the expectations of the .rtp file.

-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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