[gmx-users] How to create non-standard rediue file in GROMACS?

[Daan van Aalten]

The statement that PRODRG only uses the GROMOS-87 force field is not
correct. It can produce ffgmx, but also GROMOS96 force field files for
small molecules.

Daan

On Fri, 3 Jun 2005, Jian Zou wrote:

> junwang wrote:
>
> > Does anybody know how to create non-standard rediue file in GROMACS, ie.
> > for organic molecule? I knew the easies way to creat non-standard .top and
> > .gro files using GROMACS forcefield is to use PRODRG topology generation
> > server.
> PRODRG uses GROMOS-87 ff, not ffgmx.
>
> > Does it mean we can rename .top file to .itp file in order to create a new
> > rediue template?
> some changes should be made, you may take spc.itp in the "share/top"
> directory as an example.
>
> > Then we just need to include ffgmx.itp, the user-defined .itp and spc.itp
> > in the topology file for the whole system.
> new atomtype, bonding/non-bonding parameters should be defined in your itp.
>
> > Therefore we don't need to use pdb2gmx to create .top file any more,
> > right? After that we can just combine .top, .pdb(for the whole system) and
> > .mdp file into .tpr using grompp command. Is this procedure correct?
>
>
> hope this helps.
>
>
> Regards,
>
> Jian Zou
>
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Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
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