[gmx-users] gmx-5.0 does not seem to honour plus/minus signs in topology files
mark.j.abraham at gmail.com
Sat Jul 12 00:22:13 CEST 2014
I haven't really followed the thread, but one of
https://gerrit.gromacs.org/#/c/3686/ or https://gerrit.gromacs.org/#/c/3656/
might be a guilty party - e.g. see what happens if you check out their
On Fri, Jul 11, 2014 at 11:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> 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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