Justin A. Lemkul a écrit :
Quoting sudheer babu <[EMAIL PROTECTED]>:
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
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