Chris Sheldahl wrote:
>> Does anyone know of any parameter files for phospholipids with unsaturated
> hydrocarbon chains?
>> I'm interested in modeling POPC bilayers but the only phospholipids listed
> in the CHARMM22 topology have only saturated hydrocarbon chains. From
> this, I'm *assuming* that parameters for the unsaturated fatty acid
> carbons aren't in the CHARMM22 lipid parameter set.
The following article briefly describes the modeling of bacteriorhodopsin
embedded in a POPC bilayer:
J.A. Board Jr., L.V. Kale, K. Schulten, R.D. Skeel, and T. Schlick, "Modeling
Biomolecules: Larger Scales, Longer Durations," IEEE Computational Science &
Engineering, Vol. 1, No. 4, Winter 1994, pp. 19-30.
The above article references the following paper which probably gives more
detail:
H. Heller, M. Schaefer, and K. Schulten, "Molecular Dyamics Simulation of a
Bilayer of 200 Lipids in the Gel and in the Liquid-Crystal Phases," J.
Physical Chemistry, Vol. 97, No. 31, 1993, pp. 8343-8360.
Heller's Web page now seems to be
http://attila.imo.physik.uni-muenchen.de/~heller/ or you could contact
Schulten's theoretical biophysics group at Illinois, http://www.ks.uiuc.edu/
on the Web. Maybe some of these people could help you with the parameters.
However I don't think they used Charmm for this. Good luck.
regards,
--
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Miles Ehrlich 1111
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Asst. Editor, IEEE Computational Science & Engineering 000 111 000
10662 Los Vaqueros Circle, Los Alamitos, CA 90720 USA 000 111 000
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