By default in the CHARMM27 force field files there is no DPPC, as this
is made up from a combination of other entries in the rtp file (because
this is the way it is done in the CHARMM program's files). If you wish
to use DPPC you can construct yourself a complete DPPC rtp entry. To do
this you it is probably easiest to duplicate the DMPC entry and add the
corresponding atoms and bonds for two extra carbons in each tail.
Alternatively you could use the CHARMM36 force field (available to
download from the contributions section of the website), there should
already be an entry for DPPC.
Cheers
Tom
On 18/10/11 19:45, Justin A. Lemkul wrote:
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
--
Dr Thomas Piggot
University of Southampton, UK.
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