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

[Mark Abraham]

Hi,

We can't tell there's a problem because we know nothing about what you are
trying to do except it involves pdb2gmx

Mark

On Fri, Mar 2, 2018, 18:15 neelam wafa <neelam.wafa at gmail.com> wrote:

> 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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