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

[neelam wafa]

Is there any way to fix this problem with the start and end terminals?

On 2 Mar 2018 22:12, "neelam wafa" <neelam.wafa at gmail.com> wrote:

> Thanks  dear
>
> So it means I can continue with rest of the process. Will it not effect
> the results?
>
> On 1 Mar 2018 19:53, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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