James Starlight wrote:
Justin, hello!
In the algorthm presented in the tutorial there is one inconvenience
that is many iterations of the shrinking/minimization of the protein (
e.g if i'd like to obrain good value for S per lipid for my structure).
Is there any way to make this process automated ? ( e.g some program
wich could do all of those operations untill defined value for some
magnitudes would be reached )
Sure, you could do all of it within a shell script that loops the commands and
checks the printed output.
Also I'd like to ask about g_membed. As I've understood for that program
I need in merged pdb struture ( consist of my peptide inserted in the
membrane ) as well as merged topology. Is there any way to prepare this
data exept the way presented in your tutorial ?
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
)
That's what you obtain when concatenating the protein and membrane coordinate
files in my tutorial, prior to any inflation. You'd just have to add whatever
molecules are present in the [molecules] directive of the .top at that point.
E.g I've heard that this could also be done via PyMol. Where I could
find example of such preparation ?
I don't know of one.
-Justin
Thanks for your help,
James
2011/10/15 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
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
<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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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========================================
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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