Sara baretller wrote:
I am doing the protein in lipid tutorial .
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
Pack the lipids around the protein, i dont see where is the script perl
inflategro.pl <http://inflategro.pl>
I googled It and did not find it. Can you please send me the script or
tell me where I can find it
Then Google again :) If you search "Inflategro" it is the first result that
comes up.
Also I used the cat KALP_newbox.gro dppc128_whole.gro > system.gro
so I checked the system.gro in vmd and did not load anything. I was able
to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro
do I have to organize the system.gro because I can see that the protein
in numbered from 1 to … then the lipids start from 1 ….end .. will that
cause a problem
Numbering is irrelevant. You probably didn't clean up the file as instructed in
the tutorial:
"Remove unnecessary lines (the box vectors from the KALP structure, the header
information from the DPPC structure) and update the second line of the
coordinate file (total number of atoms) accordingly."
-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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