[gmx-users] atom naming needs to be considered.

[Justin Lemkul]

On 3/1/18 9:35 AM, neelam wafa wrote:
> Hi!
> Dear all I am running pdb2gmx command to create the protein topology but
> getting this error. please guide me how to fix this problem.
>
> WARNING: WARNING: Residue 1 named TRP of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
>
> WARNING: WARNING: Residue 264 named ASN of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.

Neither of those is an error (warnings, notes, and errors are all 
different in GROMACS), and correspond to normal output when patching N- 
and C-termini due to the deletion of atoms.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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