[gmx-users] [HELP] Residue 'NI' not found in residue topology database

[Justin Lemkul]

On 8/26/19 12:04 PM, Edjan Silva wrote:
> Dear users,
>
> I am trying to perform a simulation with a protein which contains two
> nickel atoms in the active site.
>
> When using the pdb2gmx command the following error appears:
>
> 'NI' not found in residue topology database
>
> I have edited the ions.itp file in the force field directory used (opls)
> but the same error still appears.

pdb2gmx does not read .itp files, it reads .rtp files. You need to add a 
residue definition there.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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