[gmx-users] gmx-5.0 does not seem to honour plus/minus signs in topology files

Justin Lemkul jalemkul at vt.edu
Fri Jul 11 00:46:19 CEST 2014

On 7/10/14, 6:07 AM, Michael Brunsteiner wrote:
> Hi,
> I made myself a force field for an organic polymer using a terminology/syntax
> similar to amino acids, so that i can make topoly files directly from pdb files
> using pdb2gmx.
> This worked nicely up to gmx-4.6.5, but when trying 5.0 pdb2gmx
> complains about not finding particular atoms in a pdb file, although they are
> there (only in the neighbouring residue), and then grompp gives up
> because it believes to find double entries in a angle or dihedral
> because the atom names in neighbouring resiues are identical.
> e.g. there's an entry in the angle section of resiue 2:
> "-C2 C1 C2"
> the first atom is in residue 1 the second and third are in residue 2
> (as indicated by the minus sign) but pdb2gmx/grompp believe that all three
> names refer to atoms in residue 2 and thus grompp complanes about a duplicate
> atom and givbes up ...
> Is this something that was changed in 5.0 on purpose?

I'm getting correct +/- behavior for proteins; is this maybe related to the fact 
that you have atom C2 in both the current and the preceding residue?  It would 
be useful for debugging if you could create a minimal test case that uses 
different atom names between the residues.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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