[gmx-users] (no subject)

[Bratin Kumar Das]

You need to add the particular H to the amino acid .rtp file in the
forcefield folder

On Fri, Sep 14, 2018, 4:24 PM AKANXA TIWARI <akanxatiwari24 at gmail.com>
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.
>
>
> 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$
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