James Starlight wrote:
Dear Gromacs's users!
I'd like to simulate some membrane proteins in their native environment.
Recently I've found a good tutotial of the same simulation of the KALP
peptide in DPPC membrane
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html).
Is there someone who have also tried to make thit tutorial ?
Yes, per our server logs, several hundred people have :)
First of all its very intresting for me the positioning of the protein
in the membrane via specific perl script called infrategro. What values
for the cutoff radius as well as measurements of the area per lipid
are most adequate for different membrane proteins?
The ones given in the tutorial work quite well. They are the defaults suggested
by the developers of InflateGRO.
Could you also tell me some alternative ways of full algorithm of the
protein insertion in the membrane?
Careful use of genbox (but will require significantly more equilibration as
there will be large gaps), or g_membed.
-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
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