[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 23:16:21 CEST 2014

On 7/11/14, 5:01 PM, Tsjerk Wassenaar wrote:
>> 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.
> That's not how it's done in proteins! A residue has N, and C binding to +N.

Indeed, and perhaps I should have been more clear in what I was saying.  The 
error message he's getting is related to duplicated atom indices (something I've 
never seen), and the .rtp entries have bonds for "-C2  C1" and "C1  C2" so it is 
quite likely that something in pdb2gmx is getting screwed up and it's causing 
repetition.  This is why the proteins are still a good control; the linkages are 
between non-consecutive atoms, i.e. "-C   N"  but not "N   C."



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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