James Starlight wrote:
Justin,
Could you tell me what difference in inflategro parameters ( cut-off for
lipid removing and scaling factors) should I make for insertion protein
in another bilayes in comparison tu tutorial ?
I've never made any changes; it's always worked just fine.
Now I'm working with DMPC. I've inserted symmetrical alpha helices
protein in this bilayer but inflategro deleate 2 lipid from upper and
just 1 from lower layer. It's strange because I suppose that equal
bilayer molecules would be removed :o
The number of lipids that are removed will depend on the starting configuration
of the membrane and thus where lipids are relative to the protein.
Theoretically, a symmetrical protein should delete an equal number of lipids
from each leaflet, if the geometry of the top and bottom leaflets is comparable.
Either try placing the protein at a different location to achieve equivalent
removal or manually delete a lipid and be sure to equilibrate adequately.
On Inflategro's sites I havenot found such specifity for above
parameters for different bilayers :(
The cutoffs specified are simple grid search parameters. They do not
necessarily need to be altered depending upon the lipid type.
-Justin
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
