[gmx-users] problem regarding insertion of protein into lipidbilayer

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 15 15:49:59 CET 2008

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> hi gmx users,
> i am new to gromacs , i am doing membrane protein simulations. My popc
> bilayer contain 128 molecules and protein contain 59 aminoacid residues,
> both systems i have simulated for 1ns . Now i want insert my protein into
> membrane. I have searched alot in gmxusers for how to insert protein into
> membrane and found that some are used make_hole.pl program, some of them
> have used genbox insertion command,
> The above mentioned two ways which one i have to follow,  can anyone tell
> detail information.
> Thanks in advance.

Either one should work, just be aware that make_hole.pl was designed for an
older version of Gromacs (3.1? 3.2?), and I believe some difficulties have been
reported when using it with Gromacs version 3.3.x.

To use genbox is trivial; orient your protein appropriately and use your POPC
structure as -cs input.  There have been lots of discussion about how to do
this and the problems people have faced.  No doubt you have seen these, since
you have been searching the archive :-)



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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