[gmx-users] oplsaa HISE is charged in gmx 5.1.4 and 2016
jon.kapla at icm.uu.se
Tue Nov 8 18:08:20 CET 2016
Thanks Mark and Justin,
I'll have a go at 2016.1 then.
---- Mark Abraham skrev ----
to David's first fix of https://redmine.gromacs.org/issues/2013, which was
indeed incorrect in this aspect. Justin has since fixed that, but after
5.1.4 was released. That fix will be in 5.1.5 if/when we make one. However,
you can feel quite comfortable about taking the 2016.1 share/top/oplsaa.ff
directory and using it with 5.1.x.
On Tue, Nov 8, 2016 at 4:03 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> 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),
> clearly the files are incorrect. The charges are correct in 2016.1 so
> use that version.
> > Cheers,
> > Jon
> > --
> > Postdoc, Carlsson lab
> > Dept. of Cell and Molecular Biology, Computational Biology and
> > Uppsala Biomedicinska Centrum BMC, Husarg. 3
> > Box 596
> > S-751 24, Uppsala
> > E-mail: jon.kapla at icm.uu.se
> > Phone: +46 70 3041989 <070-304%2019%2089>
> 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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