[gmx-users] pdb2gmx with GROMOS

Justin Lemkul jalemkul at vt.edu
Fri Feb 19 14:06:55 CET 2016

Can you remind me of the context here?  You've provided output files that 
indicate everything is fine.  If there's a problem with *input* please provide 
those files, the exact command and selections, etc.

I recall there was some terminus issue, but I've replied to a few hundred posts 
since then...


On 2/19/16 3:50 AM, Dries Van Rompaey wrote:
> Hi Justin,
> Sorry for the late reply. Haven't had a chance to look at this yet. Could
> you post your output files or compare the contents of yours to mine? I
> chose Gromos 54a7 as my forcefield with the SPC water model. (command line
> is gmx pdb2gmx -f 1aki.pdb).
> I'd like to know if this is a cosmetic issue or if something else is going
> on.
> My files can be found here:
> https://www.dropbox.com/sh/uapy2vxcprn0uje/AAA1TLME4czf8recVgV7U3koa?dl=0
> Thanks
> Dries
> On 1/20/16 3:48 AM, Dries Van Rompaey wrote:
>> * Hi Justin and Marco,
> *>>* Thanks for your reply. I get this behaviour when I specify the default NH3+
> *>* and COO- termini through -ter, as well as when I don't use the -ter flag.
> *>* Selecting the COOH terminus type removed the warning for the C-terminus,
> *>* but selecting the NH2 terminus type did't remove the warning for the
> *>* N-terminus. That's not a very physiological state, however.
> *>>* Can anyone replicate this error?
> *>
> I can't trigger the same with 5.1 or with current git master.  Try from a fresh
> install and make sure no one has messed with your force field files.
> -Justin
> --


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


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