[gmx-users] Atom OXT in PHE

Justin Lemkul jalemkul at vt.edu
Thu Oct 1 14:23:56 CEST 2015

On 9/30/15 1:06 PM, Sepideh Kavousi wrote:
> Hi,
> In the force fiels that you use this atom in not introduced. you have to
> import the information of atom in the atomtypes.atp file in the related
> force field you use

The error is not at all related to the content of atomtypes.atp.  The problem is 
with an incorrect or unexpected determination of a chain ending, hence 
attempting to build a COO- terminus (with atom named OXT).  Errors related to 
atom *names* are distinct from those related to atom *types* (which would show 
up in grompp more often than pdb2gmx).


> On Sun, Sep 27, 2015 at 2:15 AM, Amali Guruge <amaligg2010 at gmail.com> wrote:
>> Dear all,
>> When I give pdb2gmx command I got the following error.
>> Atom OXT in residue PHE 765 was not found in rtp entry PHE with 20 atoms
>> while sorting.
>> How can I fix this problem? Can anyone help me?
>> Thank you...
>> --
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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


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