[gmx-users] RE: Converting from AMBER to GROMACS

[Jordi Camps]

Hello,

In the process of conversion I've been making a lot of advances. Right now I
think that I only have one thing to solve. When I feed my .gro file to the
pdb2gmx in order to generate the topology, it complains about a repeated
oxygen and deletes it. This oxygen is terminal, and the same pdb2gmx adds
another one in slightly different coordinates. If I reprocess the output
(conf.gro) with the same program, the same problem occurs.

Is there any way to get the pdb2gmx understand which is the terminal oxygen
and not rewrite another one?

The warning is like this:
	Checking for duplicate atoms....
	deleting duplicate atom    O  LEU 130

The input file is:
...
  130LEU      C 1967   4.006   4.529   2.877  0.0016  0.0158  0.0498
  130LEU      O 1968   3.998   4.478   2.988 -0.0007 -0.0469 -0.0096
  130LEU    OXT 1969   4.044   4.466   2.773 -0.0345  0.0014 -0.0298
  131NA      NA 1970   2.161   2.836   4.117 -0.0074 -0.0084 -0.0245
 
...

And the output file is:
...
  130LEU      C 1967   4.006   4.529   2.877
  130LEU     O1 1968   4.050   4.460   2.768
  130LEU     O2 1969   3.956   4.474   2.991
  131NA      NA 1970   2.161   2.836   4.117
...

Thanks for your help.

--

Jordi Camps Puchades

Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
UPC-CIRI
c/. Jordi Girona 1-3 
Modul C6-E201                     Tel. : 934 011 650
E-08034 Barcelona                 Fax  : 934 017 014
Catalunya (Spain)                 e-mail: jcamps at lsi.upc.edu