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 53a6_carbo. 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.
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
