[gmx-users] (no subject)

[Tushar Ranjan Moharana]

Hi everyone,
I want to simulate lid opening of lipase in presence of micelles of
triglyceride having both saturated and *cis* polyunsaturated fatty acids
(separately). When I did it using GROMOS 54a7 I didn't get appropriate
result. It seems as if the forcefield doesn't considered unsaturation. When
I use CHARM36 everything was fine till energy minimization but when I did
nVT or nPT simulation the unit cell which was a cube becomes a rectangular
slab and the worse thing was all the triglyceride molecule goes out of the
unit cell. When I try OPLSAA I am getting "No default Proper Dih. types"
also the total charge is non integer.I use topolbuild 1.3 to create .itp
file of my triglyceride. Please let me know Which forcefield I should use
and how shall I make .itp (or topology) file for triglyceride containing
*cis* polyunsaturated fatty acid (for example EPA or DHA) and any other
modification I shall do to any file of that forcefield.

Any help or advice will be precious to me
Thanks for your time and effort
-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB