[gmx-users] (no subject)

[AKANXA TIWARI]

thanks for reply


On Fri, Sep 14, 2018 at 5:09 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/14/18 6:48 AM, AKANXA TIWARI wrote:
> > i am getting a warning after converting pdb2gmx and then applying force
> > field what i will do. please help me.i get this on screen.
> > WARNING: WARNING: Residue 1 named ALA 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 374 named PHE 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.
> >
>
> pdb2gmx is just being a bit too noisy here. Termini are being patched,
> which means some atoms get deleted, replaced, or added. Here, an
> existing atom is being deleted and replaced with another at both the N-
> and C-termini. There is no problem, as you see the message below about
> successful completion.
>
> -Justin
>
> > Before cleaning: 6050 pairs
> > Before cleaning: 7868 dihedrals
> > Making cmap torsions...
> > There are 2709 dihedrals, 1833 impropers, 5404 angles
> >            6050 pairs,     3705 bonds and     0 virtual sites
> > Total mass 40604.576 a.m.u.
> > Total charge 11.000 e
> > Writing topology
> >
> > Back Off! I just backed up posre.itp to ./#posre.itp.1#
> >
> > Writing coordinate file...
> >
> > Back Off! I just backed up actin_asp_processed.gro to
> > ./#actin_asp_processed.gro.1#
> >          --------- PLEASE NOTE ------------
> > You have successfully generated a topology from: actin_asp_clean.pdb.
> > The Gromos54a7 force field and the spce water model are used.
> >          --------- ETON ESAELP ------------
> >
> > GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)
> >
> > akanxa at akanxa-HP-Notebook:~/Documents/aasp$
>
> --
> ==================================================
>
> 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.thelemkullab.com
>
> ==================================================
>
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