----- Original Message ----- From: Tsjerk Wassenaar <[email protected]> Date: Friday, July 2, 2010 14:10 Subject: Re: [gmx-users] B-factor To: Discussion list for GROMACS users <[email protected]>
> 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. Mark > 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
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