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

[junwang]

Dear GROMACS developers and users:

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. 
Does it mean we can rename .top file to .itp file in order to create a new rediue template?
Then we just need to include ffgmx.itp, the user-defined .itp and spc.itp in the topology file for the whole system. 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?


Best regards,
Sincerely,
Jun WANG

Department of Chemistry
University of Nebraska-Lincoln
536 Hamilton Hall
Lincoln, NE 68588-0304
U.S.A.
E-mail:junwang at unlserve.unl.edu
       junwang at bigred.unl.edu