Can this help? http://www.gromacs.org/pipermail/gmx-users/2006-March/020599.html I found using the users-gmx mailing list archives (you should search the archive before posting): http://www.gromacs.org/component/option,com_wrapper/Itemid,165/
If that doesn't solve your problem, you can always write some short PERL script to do the renaming for you. Good Luck, -Shay Amram -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ragnarok sdf Sent: Sunday, August 10, 2008 19:05 PM To: [email protected] Subject: [gmx-users] AMBER and gromacs atoms renaming Hi, I am running a simulation of a protein DNA complex, and for this i am using AMBER99 forcefield. The problem is that every complex I need to run, I have to rename several residues and atoms, especially hydrogen atoms one by one (well, actually using replace tool). And this takes hours to get done. Is there any shortcut I can use, like a software that prepares my pdb files for an AMBER run, or something close to that? If not, Ill just keep doing things by hand. Thank you FabrÃcio Bracht _______________________________________________ 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 _______________________________________________ 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
