Check the manual for 'genbox'. Once you work out how to use it, remember to check your output for waters within the bilayer - I'm not sure how big the cavities are, but I wouldn't be surprised if you could fit a water molecule or two in.
----- Original Message ---- From: naga raju <[EMAIL PROTECTED]> To: [email protected] Sent: Friday, June 1, 2007 8:07:08 AM Subject: [gmx-users] Regarding membrane protein solvation Dear gmx users, I inserted mebrane protein in DOPC lipid bilayer, some part of protein is outside of lipid bilayer. Would you tell me how to add water molecules to protein(to the out side of lipid bilayer part) around 6 angstroms radius. any suggestion is appreciated. with best regards, Nagaraja. ____________________________________________________________________________________ Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL _______________________________________________ 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 ____________________________________________________________________________________ Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL _______________________________________________ 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
