[gmx-users] add new atom

[Justin Lemkul]

On 1/28/16 12:50 PM, Malihe Hasanzadeh wrote:
> Hi
> I want to do a Pr-Ligand MD simulations by gromacs 5.0.5. My protein has
> two Ni ions. I added parameters of Ni to ffnonbonded.itp , atomtypes.atp
> and ions.itp. I also added "Ni Ion" to residuetypes.dat. But when I run
> pdb2gmx, gives this :Warning: Starting residue NI571 in chain not
> identified as Protein/RNA/DNA".
> Could you please help me what id my mistake?

I don't see one.  An ion is not protein/RNA/DNA, so pdb2gmx is just telling you 
that a new chain has started with something new.  Maybe it shouldn't say 
"warning" ("note" might be better), but unless there's something that actually 
says "error" then you likely don't have a problem here.

-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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