[gmx-users] Use of non-standard CHARMM27 forcefield in Gromacs - how?

[Justin A. Lemkul]

Jernej Zidar wrote:
> Dear all,
>  During my PHD studies we developed a specific lipid force field
> based on the CHARMM27 force field containing spingomyelin molecules of
> various saturation and chain lengths.
> 
>  Now I would like to use this forcefield in Gromacs but I don't know
> where to start. Is there a way to import it into Gromacs? The files
> used in the Charmm simulations were:
> top_all27_lipid.rtf
> par_all27_lipid.rtf
> toppar_all27_lipid_cholesterol.str (the one containing the specific
> sphingomyelin bits)
> 

You will need to convert the contents of these files to Gromacs format.  Force 
field organization and topology format are discussed in Chapter 5 of the manual. 
  There is no substitute for a thorough working knowledge of this material. 
There are some old scripts on the Gromacs website (under "User Contributions") 
that you might be able to co-opt to convert between CHARMM and Gromacs formats.

In the end, you need to add any new bonded and nonbonded parameters, atom types, 
etc into the force field (top level) files, and then create a molecule topology 
(.itp file) for your lipid.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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