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

[Jon Kapla]

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?

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