[gmx-users] Adding GROMOS force field to pdb2gmx

Marc Gordon marcgrdn55 at gmail.com
Sun Apr 15 13:54:39 CEST 2012

Here is a brief summary of my situation:

>From what my copy of gromacs tells me pdb2gmx is using a 53a6 forcefield
from 2004.
I want to use the more recent carbohydrate specific 53a6_carbo force field.
I have only managed to find this force field in GROMOS format.

What I ultimately want is just the gromacs input topology files etc.
generated by pdb2gmx (or some other equivalent application). I don't intend
to actually run the simulation in gromacs, for that I will be using NAMD
but I need the gromacs input files in order to perform the run through

So as far as I can see I have a few options and I wanted to seek the advice
of those with more experience than myself in the use of gromacs and
associated applications:
1. someone has done this already and is willing to share
2. convert GROMOS force field format (.mtb and .ifp) into gromacs format
(.rtp, .itp, .atp etc.) and then incorporate that into pdb2gmx - if some
sort of application exists for this then great otherwise it seems like a
rather complicated task (not the incorporating but the converting)
3. amend the existing 53a6 force field in pdb2gmx to incorporate the
desired carbohydrate elements - is such a thing possible?
4. use something other than pdb2gmx that performs the same function

Any suggestions would be appreciated.
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