James Starlight wrote:
Justin
Sure, you could do all of it within a shell script that loops the
commands and checks the printed output.
As I understood in that iterations only step with scalling by factor
0.95 and futher energy minimization must be included until desired S per
lipid will be reached. Could you provide me with a small example of such
script for better understanding of the syntax. I've never done unix's
shell scripts before :)
I don't have one on hand, sorry. An hour or so spent with shell scripting
tutorials will probably lead you to it, though.
Could you tell me where I could found experimental valuee for Area per
lipid for differen cases (e.g I'll be work with large membrane proteins
such as membrane receptors so i wounder to know what values of S per
lipid as well as S per protein I might expect in that case)
Some are given in the tutorial, along with references. If you're a lipid that's
not listed, you'll have to find such information in the literature.
Also I have a question about solvation of my membrane protein via
GENBOX. I found 2 possible ways to exclude water from the insertion into
membrane
- Changing vdv radii for the C atoms- So i've copied vdwradii.dat to my
work dirrectory and changed vdv R. How I should to define that genbox
uses exactly that modified file located in my working directory instead
of default vdwradii.dat? Finally how I can check that there are not
waters within the membrane ? (I've tried to visualize via VMD but the
overal picture is very unclear :) )
The working directory is always searched first. This is true for all Gromacs
programs. Visualization is the only way to tell. Perhaps you need to render a
more clear image. Simply loading the .gro file and not making any refinements
to the representation is a good way to go cross-eyed :)
- Also I've found that I can Running short md to exclude those waters
via hyfrophobic effect. What parametries would be opti,al for that
simulation in case of KALP as well as other more larger proteins ?
The same parameters that you would use to run normal MD on such a system;
there's nothing special about this procedure. Restraints would be advisable.
-Justin
Thank you for your help,
James
--
========================================
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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