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

[neelam wafa]

I am trying md simmulation of a protein kinase and ligand to check the
stability of the protein ligand complex formed.

On 2 Mar 2018 22:22, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> 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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