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

[Stéphane Téletchéa]

Justin A. Lemkul a écrit :
> 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

Consider also inflategro.pl and its accompanying paper, you'll save a 
lot of time in the beginning.

Both info at http://moose.bio.ucalgary.ca/index.php?page=Programs

Cheers,
Stéphane

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901