James Starlight wrote:
Greetings!
Recently I've found that Charmm27 ff is widely used for the simulation
of the membrane proteins. I've tried to work with pure DPPC bilayer in
pdb2grx and obtain that charm27 ff included in the Gromacs is lack for
the parametries for the lipids.
Could you tell me where I could obtain those parametries ( and tutorial
of how it might be included in processing of lipids) or full functional
charmm27 ff that already has pre-built those parametries?
Most of the common lipids are already present in lipids.rtp in charmm27.ff in
Gromacs 4.5.x; if you are looking for lipids not present there, please be more
specific as to what you need.
The only membrane protein tutorial to my knowledge is my own. Dealing with
CHARMM should be significantly easier, however, as no modification of the force
field is necessary. Run pdb2gmx on a single lipid molecule, convert the .top to
.itp (see the wiki) and #include it in the .top for your protein, just like in
my tutorial.
-Justin
Thank you for help
James
--
========================================
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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