Vijayaraj wrote:
Hello,
I need to simulate a peptide in nonane solvent environment using ff99SB
force field. As there are different procedures used to create a solvent
box, different from water, specific to several force fields, I would
like to make sure the method which I am going to use will be appropriate
for my simulation. here is the procedure,
1. Nonane parameters using GAFF with python interface to antechamber
(acpype), this program generates gromacs compatible amber ff.
2. solvent box with nonane using gromacs with appropriate box dimension
and NPT equilibration.
3. Insertion of the peptide to the equilibrated nonane solvent box.
This seems reasonable to me.
-Justin
--
========================================
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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