Hi, >> ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41 > > The last column is the occupancy (1.00) and temperature factor numbers > concatenated. You can fix the symptoms by editing the file by hand so that > these numbers occupy the right columns - see the PDB format. > > This illustrates buggy behaviour from GROMACS. src/tools/gmx_rmsf.c probably > needs to call set_pdb_wide_format(TRUE) before write_sto_conf_indexed(). > Please file a bugzilla (see GROMACS webpage). >
I disagree. The PDB file is fixed width, and the format for the b-factor field is %6.2f. This means that the above line is a proper PDB ATOM definition. Using the Gromacs pdb_wide_format generates a PDB file that may not be compatible with other programs. I would argue though that Gromacs should at least warn when trying to write numbers larger than 999.99 to the b-factor/occupancy field. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.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
