[gmx-users] B-factor

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jul 2 06:10:01 CEST 2010


>> 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.



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list