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

[Anton Feenstra]

Jordi Camps wrote:

> 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?

Not that I know of. The first step, deleting the oxygen, is part of the 
initial consistency check of your input file. At this stage, it is hard 
to make pdb2gmx already aware of a possible carbonyl group at the terminus.

You can always paste back in the coordinates from your input file, into 
the pdb2gmx output file...


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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