chris.ne...@utoronto.ca wrote:
Use gromacs 3 for the editconf -princ step.
Or, if using Gromacs 4, apply a 90-degree rotation, as I indicate in the
tutorial.
-Justin
-- original message --
Dear justin
Thanks for tutorial on membrane protein simulation . I
am following your tutorial, everything is fine but problem came in
concatanation . After orrienting the protein by using editconf
I did the concatanation process everything is fine but the file which I got
after concatanation i.e system.gro when I viewed this file in pymol the
insertion is totally wrong the protein inserted parallel to bilayer
hydrophobic core it is totally wrong I need protein should inserted
perpendicular to lipid bilayer i.e from one side polar head of lipid to
another side by crossing hydrophobic core of lipid .
can u suggest me right method to insert my protein into lipidbilayer in
proper orientation before using inflategro methedology.
I am just stuck on that point .
I am eagerly waiting for your reply.
Thanks a lot in advance.
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use thewww
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
