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 ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
