[gmx-users] can not split pdb beyond 1019

Mark Abraham mark.j.abraham at gmail.com
Mon Oct 6 19:52:52 CEST 2014


Thanks, good report. Unfortunately, someone in prehistoric times
implemented the functionality common to -sep and -split using the or
operator... everywhere except closing the file. So -split will continue
opening files until it runs out of file handles (so later on, files can't
be opened), and maybe accidentally write something to disk, depending how
the OS works. I've uploaded a fix for a future 5.0.x version.


On Mon, Oct 6, 2014 at 4:18 PM, gromacs query <gromacsquery at gmail.com>

> Hi All,
> I am trying to split my trajectory in single frame pdbs for some analysis
> using trjconv but it ends with an error after ouput 1019 pdbs. I tried with
> different version of gromacs (4.6.3 and 5.0) its the same error.
> trjconv -s ../em.tpr -f ../image_fitted.trr -o test.pdb -split 10 -b 40000
> -e 96000 -n ndx.ndx
> error
> /src/gmxlib/futil.c, line: 1032
> Fatal error:
> Library file residuetypes.dat not found in current dir nor in default
> directories.
> Why 1019 is a magic number? Even I tried changing -b where trjconv stopped
> reading. It seems what ever part of trajectory I choose it ends always at
> 1019 frames. Also error (Library file residuetypes.dat not found in) does
> not seems to be correct as if it would have been the case then I should not
> have got any frame read.
> Thanks for any help
> JIom
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list