The script that deals with converting trajectories is trjconv. Have a look at the documentation, that will show you the formats it can handle, no idea what Amber format is, but as long as you can get it into one of the ones it can use should be fine. Plus, with g_cluster I suspect you will require a topology file to be able to do the analysis, which will be your major sticking point.
Note that pdb2gmx converts pdb coordinate files to generate a topology file (and the residues/molecules have to be known by the database otherwise you have to make by hand etc). Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
