[gmx-users] How to create non-standard rediue file in GROMACS?
zouj01 at mails.tsinghua.edu.cn
Fri Jun 3 11:48:37 CEST 2005
> 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
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.
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