[gmx-users] oplsaa HISE is charged in gmx 5.1.4 and 2016

Justin Lemkul jalemkul at vt.edu
Tue Nov 8 16:03:36 CET 2016

On 11/8/16 9:54 AM, Jon Kapla wrote:
> Hi everyone,
> I’m trying to setup topologies for OPLS-aa simulations with GPCRs. When running pdb2gmx in gromacs 5.1.4 (and gromacs 2016) the total charge of a specific GPCR ends up at 2.435e. Running gromacs 4.6.7 results in the same protonation, but a more reasonable integer charge of 3e.
> I have investigated the issue, and it seems that the difference is stemming from differing atom charges in the HISE residue in aminoacids.rtp. If I sum up the atom charges in HISE (5.1.4) I find that it actually is charged by -0.113e, which exatly corresponds to the difference in the reported charge from pdb2gmx (5 HISE * -0.113).
> Is this a known problem?

This should have been fixed for 5.1.4 (and the release notes say it was), but 
clearly the files are incorrect.  The charges are correct in 2016.1 so please 
use that version.


> Cheers,
> Jon
> --
> Postdoc, Carlsson lab
> Dept. of Cell and Molecular Biology, Computational Biology and Bioinformatics
> Uppsala Biomedicinska Centrum BMC, Husarg. 3
> Box 596
> S-751 24, Uppsala
> E-mail: jon.kapla at icm.uu.se
> Phone: +46 70 3041989


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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