[gmx-users] NVT Equilibration error

[Justin Lemkul]

On 5/5/15 2:31 PM, Agnivo Gosai wrote:
> Hello,
>
> The PDB code of my structure is 1HAO.
>
> http://www.rcsb.org/pdb/explore/remediatedSequence.do;jsessionid=49DB9DA4F66D6A5F19554FBC6741967D?params.chainEntityStrategyStr=all&structureId=1HAO
>
> Thrombin has got 2 chains and the atoms mentioned in the warning are in the
> heavy chain. Residues 229 and 230.
>

Keep in mind that the atom numbers pdb2gmx writes are for the post-processed, 
H-added structure.  So they are not what you see in the PDB file.  In this case, 
atoms 2429 and 2431 correspond to residues 148 and 150 - note there's a missing 
residue in between!

-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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