[gmx-users] ATP all-atom FF in GROMACS (CHARMM36?)

[Justin Lemkul]

On 2/19/13 1:29 PM, Bryan Roessler wrote:
> Hello,
>
> I am trying to locate an all-atom FF for ATP that I can use in GROMACS. The
> ATP residue is stored in a toppar stream file in CHARMM, thus it is not
> included in the download on the user-submission page for FFs. It also
> appears that it is not available in the AMBER forcefields.
>
> It is however, present in the GROMOS FF supplied with GROMACS and also
> available on the user-submission website. However, I have reservations
> about using a united-atom FF in conjunction with CHARMM (which is how the
> rest of my system is parameterized). I've also taken a PDB of ATP and

Mixing and matching is always a terrible idea, especially when the force fields 
in question share basically no attributes in common.

> parameterized it with SWISS-PARAM, however the user-submitted
> 'CHARMM2GROMACS' scripts are not successfully parsing the
> topology/parameter files and not generating valid GROMACS output.
>
> If anyone has a CHARMM FF for ATP that is in >GROMACS4.5.4 format, I would
> be much obliged. If it is not available, I could use some help in
> understanding how to convert toppar stream entries from CHARMM into the
> GROMACS format.
>

Googling turns up a few results, at least one of which may be of particular 
interest:

http://gromacs.5086.n6.nabble.com/Nucleotides-for-charmm-port-td4444934.html

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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