I have made a popg:pope bilayer lipid via charmm gui online for molecular dynamic purpose. But i could not pack my lipid via inflate script because it works only for ine type lipid.
It's just a matter of creating an array for the lipid types and looping over them.
But you can build the entire membrane protein system in CHARMM-GUI; there's no need for external tools.
Dear Justin
I built the entire membrane protein, but I have to packing lipids around an embedded protein to analys it`s interaction with my target protein with gromacs.
Dear Dr. Zaeifi,
I think, it's not a good idea to use InflateGRo especially when u r working on mixed lipids. I ll recommend u to use g_membed program. It is bit tricky, but I guess u can make it. The crucial thing is to input a perfect box dimension in the editconf format.
P.S. Pls don't mind for my shorthand in the text.
Regards
Bikash
Dear Bikash
I have used it before, but it could not help out too. know I am trying to use Inflategro2 to solve the problem.
Thank you all.
Dear yogesh
Yes, but you sould use inflateGro2 in the case of Mixed membrane bilayer. Consider the link below for more info ...
http://pubs.acs.org/doi/abs/10.1021/ci3000453
great, it works for me :) only areaperlipids.dat files were not generated...
Final area per lipid could calculated by another software, as you can search in the web, like GridMat-MD depends on calculation flat membrane or Vesicle one by FATSLiM .
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