[gmx-users] parameters for unsaturated fatty acids

[Shang-Te Danny Hsu]

Dear all,

I have been trying to setup simulations involving polyunsaturated lipid 
tail. FOr example:

-(-CH2-CH=C(CH3)-C-)n-

The trans/cis geometry around the double bond should make some 
differences....

So far the only updated parameters for lipids are mainly devoted to 
saturated groups, LCH2 and LCH3. Only few publications are dealing with 
these types of lipids (e.g. JACS,124(2):298; JACS,124(2):318) but they 
are developed for CHARMM force field. I am wondering how I should 
implement these parameters for GROMACS. Because this lipid molecule is 
not easy to produce in large scale, therefore, deuteration is not 
feasible to obtain experimental NMR/thermodynamics data for validation. 
Has anyone got any suggestion?
-- 
Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl