[gmx-users] Crystallographic Ions

[Justin Lemkul]

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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