On 15/04/2012 9:54 PM, Marc Gordon wrote:
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)
Useful conversion programs tend to be rare, but they do exist. No idea
if one useful for you exists. Google hard, and contact the authors of
the force field to see what they know about who might have anything useful.
3. amend the existing 53a6 force field in pdb2gmx to incorporate the
desired carbohydrate elements - is such a thing possible?
Yes, the last para of the approach here
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
is appropriate to this. If there's only a small subset of the changes to
53a6 that are relevant for your simulation, this is probably the
simplest approach.
Mark
4. use something other than pdb2gmx that performs the same function
Any suggestions would be appreciated.
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