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
--
========================================
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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