[gmx-users] NA or SOD in CHARMM36
jalemkul at vt.edu
Thu Apr 21 11:47:18 CEST 2016
On 4/21/16 4:56 AM, Jason Loo Siau Ee wrote:
> Hi all,
> I'm trying to simulate a protein-ligand complex in POPC membrane using the CHARMM36 forcefield, which I got from the Mackerell site and included in /share/gromacs/top/. Now when I run grompp I get the error "Fatal error: No such moleculetype SOD" despite the fact that I have #include "charmm36.ff/ions.itp" in my topology. A quick check on the ions.itp in charmm36.ff/ shows the following:
> [ moleculetype ]
> ; molname nrexcl
> NA 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 SOD 1 NA NA 1 1
> Now as I understand sodium is called SOD in CHARMM, so shouldn't all the NA be SOD instead? As this is from the Mackerell site I'm going to assume there isn't an error here, so am I about the do something silly? Is there a reason for this discrepancy (like because genion only adds NA and not SOD)? I've noticed similar issues with other ions and the water models (SOL instead of TI3P). I'm guessing I should create a local copy of the modified itp files then?
You should use NA; this is done to follow the GROMACS genion convention that
ions are added by their all-caps elemental symbol. So your -pname in genion
should be NA, which means NA is written to the topology file. SOD is just the
atom type, which is only used by grompp when parsing the actual parameters.
You shouldn't need to make any changes to the files.
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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