Nancy wrote:
Hello,
More specifically, I am unsure as to the procedure of inflating and
minimizing a bilayer using "InflateGRO". In the tutorial at:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
I followed it successfully up to the inflation step, but I do not know
specifically what parameters to run the energy minimisation. Please advise.
Most general EM .mdp files are suitable; a simple one is linked in Step 1 on the
page you quote above, "Orient the protein and membrane;" modifications that
should be made to it are described in Step 2, "Pack the lipids around the protein."
The caveat to my membrane protein tutorial was that the user should already be
used to normal input/output routines with Gromacs. A simpler tutorial to
familiarize you with Gromacs procedures can be found at:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
It might be useful if you are unfamiliar with simulation protocols with Gromacs,
since it is conceptually easier and more detailed in the description of each
step. If the minimized bilayer is not showing up as inflated, then you probably
invoked InflateGRO incorrectly (hence why I asked for the command lines you
invoked). Usage is described in the text of the inflategro.pl script, and I
describe typical scaling factors that should be used for the procedure in the
tutorial.
-Justin
Thank you.
Nancy
On Wed, Jul 29, 2009 at 7:49 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Nancy wrote:
Hello,
I am trying to run energy minimisation on a lipid bilayer
(downloaded from:
http://moose.bio.ucalgary.ca/files/dppc128.pdb). I inflated the
bilayer using "InflateGRO" however, when I try to run the
minimisation, it seems to display the un-inflated bilayer.
Please advise.
Without seeing the command lines that you're issuing, we can only
assume you are doing something wrong.
-Justin
Thank you.
Nancy
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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