xi zhao wrote: > Dear all users: > I want to simulate a system ( protein + chromophore). I > have had chromophore.gro and its top file using amb2gmx.pl,but I find I > can not use them to translate PDB( protein + chromophore) file into gro > and top files properly. So I need your advice about further procedure! > Thank you very much
You don't need a .gro file. See http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file The grompp utility will happily make a .tpr from your .mdp, your .top file, and your well-formed .pdb file whose atom, residue and molecule names and ordering matches the .top file. This last constraint also applies to a .gro file! Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
