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

[Jian Zou]

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