[gmx-users] Atom OXT in PHE
jalemkul at vt.edu
Thu Oct 1 14:23:56 CEST 2015
On 9/30/15 1:06 PM, Sepideh Kavousi wrote:
> 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...
>> Gromacs Users mailing list
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users