[gmx-users] NA or SOD in CHARMM36

Justin Lemkul 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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