Pablo Englebienne wrote:
Hi all,
I'm trying to simulate a small molecule in a chloroform box using the
GROMOS G53a5 forcefield. I realized that the parameters for the solvent
are present in the ffG53a5.rtp file, however I could not find a CHCl3
solvent box included in GROMACS. I did find, however, a CHCl3 solvent
box equilibrated by PeiQuan Chen
(http://lists.gromacs.org/pipermail/gmx-users/2003-May/005572.html) at
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
.
I also saw mention of a box for the Amber forcefield, that is now
included in AmberTools (amber10/dat/solvents/cform/cform.pdb and
chcl3_equil.pdb.1). I took this one and I'm equilibrating it to use it
later.
In the mean time, I wanted to know if I overlooked something, and there
is a CHCl3 box to use with the GROMOS forcefield?
Not one that is officially distributed. If it was, it would be the
/share/gromacs/top subdirectory with other solvent topologies and structures.
Probably your best bet is to use the one in the User Contributions section,
unless you feel the need to create your own and start from scratch.
-Justin
Thanks!
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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