[gmx-users] B-factor

Mark Abraham mark.abraham at anu.edu.au
Sun Jul 4 13:30:11 CEST 2010

----- Original Message -----
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Date: Friday, July 2, 2010 14:10
Subject: Re: [gmx-users] B-factor
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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

True. I misread what was happening with the pdbform variable and leapt to a conclusion. The observed GROMACS behaviour now looks correct. I don't recall what symptoms the OP had, but presumably they were related to the function of the correctly-formatted file with some (other) software that assumes space-delimited PDB fields.


> 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
> -- 
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