[gmx-users] How to resolve OXT atom issue?

Justin Lemkul jalemkul at vt.edu
Mon Dec 19 02:31:12 CET 2016

On 12/17/16 1:34 AM, Seera Suryanarayana wrote:
> Dear Justin,
> I apologize you as I am wasting your  valuable time.
>   I have peptide with 69 residues and some of the SER and THR residues
>   are phosphorylated and also some of the missing residues(1 to 6; 36 to 41
>   and 69) have been modeled by modeller . I have chosen charmm36 force
> field.
>   When I executed the command
>   pdb2gmx  -f 1th1.pdb -o 1th1_processed.gro -water spce -ignh
>   I got following error.
>   Fatal error:
>    Atom OXT in residues GLU 69 was not found un rtp enrty GLU with 15
>    atoms while sorting atoms.
>  Here I am sending a link which has the coordinate file.
> https://drive.google.com/file/d/0B5HyqLWajWjHWjMyY25Cc3lSRTA/view?usp=drive_web

You still have some misnamed residues, but I took the time to correct them so we 
can arrive at a solution at long last.  The problem here is that you need to add 
SP1 and THP1 to residuetypes.dat to have them recognized as protein.  Once you 
do that, it works fine.  Discontinuous chains cause all manner of problems; this 
is just one of the more cryptic ones.



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


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