[gmx-users] Fatal error

[Justin Lemkul]

On 5/6/15 7:55 AM, Urszula Uciechowska wrote:
>
> Hi,
>
> I am trying to run pdb2gmx by using:
>
> pdb2gmx -f COM-oH.pdb -o COM-oH.gro -p COM-oH.top -ignh -water tip3p -ter
>
> however I am getting a fatal error:
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.3
> Source code file: pgutil.c, line: 99
>
> Fatal error:
> Atom C not found in residue seq.nr. 137 while adding atom
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "(That makes 100 errors; please try again.)" (TeX)
>
>
>
> I have checkec the 137 AA and there is C atom. The system consist of DNA
> and 3 protein receptors. I used  6: AMBER99SB-ILDN force field. What is
> wrong here?
>

You have a missing atom.  Make sure you're looking at the right residue; if you 
have multiple chains it can be simply in another chain with that residue (and I 
believe pdb2gmx renumbers the chain internally, anyway).

-Justin

-- 
==================================================

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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