After doing the 'pdb2gmx', created the cell e filled with solvent, use the "make_ndx" to create an index of your system. One of the groups should be your residues that you want to freeze. Then, in your .mdp file, use 'freezegrps' and 'freezedim' in your recently created group.
Don't forget the -n yourindexfile.ndx in the grompp command line. It should work. Good luck! -- Marcelo Depólo Polêto Bolsista FAPEMIG Laboratório de Infectologia Molecular Animal - LIMA Departamento de Bioquímica e Biologia Molecular Universidade Federal de Viçosa - UFV Tel.: +55 31 3899-2911/2912 MSN: [email protected] <[email protected]> *Website: http://opensourcebioinformatics.com/site/* -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
