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

[Mark Abraham]

Hi,

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
respective parents.

Mark


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
>> +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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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