[gmx-users] Crystallographic Ions
jalemkul at vt.edu
Wed Sep 23 00:44:31 CEST 2015
On 9/22/15 3:27 PM, Parker de Waal wrote:
> Hi Everyone,
> I'm working with a protein which contains 2 crystallographic sodium ions and am experiencing trouble making the .gro file using pdb2gro using the Charmm36.ff parameters.
> The two ions can be seen here:
> ATOM 29009 NA NA 1 -18.056 -14.113 -24.865 1.00 0.00
> ATOM 29010 NA NA 2 27.831 26.294 -32.202 1.00 0.00
> Whenever I run pdb2gro the program complains that NA is not a valid atom type, however whenever I manually change the ions to atom and res type to SOD the resulting .top file does not count the molecules correctly.
> [ molecules ]
> ; Compound #mols
> Other 1 (should be NA+ and 2?)
Look at the .itp file for "Other" and you will see that there will be two SOD in
that [moleculetype]. "SOD" is the .rtp entry (according to standard CHARMM
nomenclature) but "NA+" is the genion convention (and hence what is used in
ions.itp). There is no difference between the two.
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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