[gmx-users] start gromacs membrane more protein simulation

Antonio Sergio Kimus Braz askbraz2list at gmail.com
Wed Sep 21 02:15:09 CEST 2005


I am beginner in the GROMACS

I am trying to simulate a theorical model of a pump protein in explicit  
lipid bilayer membrane environment (DMPC or POPC), I have the pdb
files of this protein and membrane , I have to topolies files this
lipids (dmpc.ip or popc.itp)…I also saw  the mdrun_make_hole.tar.gz in
(http://www.gromacs.org/contributions/index.php) ..
However my doubt stays, 
n which stage I do enter with membrane files? pdb and itp.

don't get to generate files type .gro or .top, starting from the
membrane alone or membrane more protein pdb files, using pdb2gmx or
editconf commands…

I also tried to insert the membrane using the genbox command with –ci
option with dmpc.pdb

I don't really know as creating an input files membrane + protein for
run in gromacs…

Anybody could help ?

thank you very much !

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