[gmx-users] parameters for unsaturated fatty acids

[David van der Spoel]

On Wed, 1 May 2002, Shang-Te Danny Hsu wrote:

>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?
Generally speaking, if your double bond is localized, which it probably is
in this case, you want to have an improper dihedral to keep it in cis
conformation, or a normal dihedral with multiplicity 2 and large force
constant (check peptide backbone omega angle). As for Van der Waals
parameters, I don't know whether the difference are so large that you need
to worry about them. Actually I'm prettyr certain people have done that
with gromacs, so check papers by Van Buuren and Marrink.


Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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