[gmx-users] (no subject)

[Justin Lemkul]

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

==================================================