[gmx-users] residue database

Xavier Periole x.periole at chem.rug.nl
Tue Jul 6 19:32:39 CEST 2004

Dinesh Pinisetty wrote:

>Hello everybody,
>       When I asked for the residue that was missing 'MeO' and the atom
>under it 'Me1',I was given a reply to use prodrg server or to add the
>residue and atom manually.
>   I cannot add this atom or the residue manually as I do not have the
>information about the atom.So I tried using prodrg server,now the problem
>is even this server does not recognize the atom Me1.Its not executing the
>pdb file.
> Please suggest me what to do now to get the topology and coordinate
>files.By the way these files where readily created in the tutor of Gromacs
>so please someone help me out in explaining me the procedure in which it
>was created and giving me information about the atom
>Me1(bonds,charge,charge groups,improper dihedrals etc)what all are
>applicable to this atom and which all are required to add this in
> Thanks in advance...........
I have not followed the discussion (I was away) but I use methanol in
some simulations and have no problems. The residue in the gro file is
called MeOH and the atome names are Me1, O2 and H3. Using the methanol.itp
and the ffG43a1 force field.

Hope it helps


   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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