[gmx-users] Adding GROMOS force field to pdb2gmx

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 15 15:11:47 CEST 2012

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 
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.


> 4. use something other than pdb2gmx that performs the same function
> Any suggestions would be appreciated.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120415/a00d2d59/attachment.html>

More information about the gromacs.org_gmx-users mailing list