[gmx-users] Protein simulation including ligand with Fe(III)

[Justin Lemkul]

On 8/6/14, 12:50 PM, Nikolaos Michelarakis wrote:
> Thanks a lot. Didn't realize that this would affect the topology.
>
> I now get an error that Fe is not in the residuetype.dat file. Since
> Gromos96 has parameters for Fe, shouldn't it be in the file? Just wondering.
>

Only things defined as residues in the .rtp file need to be included in 
residuetypes.dat.  If you introduce FE in the .rtp, you need to add it as a 
known residue with a type of Ion.

-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 601
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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