[gmx-developers] trjconv doesn't check if the .tpr, .xtc, and .ndx files provided match

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 31 06:49:11 CET 2014

Hey :)

The index file only contains labels and numbers. The labels are for you to
make sense of and allow easy referencing. There is nothing in the
reference/trajectory/index that allows checking whether the indices match
what you mean.



On Fri, Jan 31, 2014 at 4:16 AM, sryckbos <sryckbos at stanford.edu> wrote:

> trjconv doesn't seem to check whether the .ndx file you specify corresponds
> at all with the .tpr and .xtc files you input.  I wrote a script that was
> using trjconv to remove the waters from many of my trajectories on several
> different systems.  I made an .ndx file for each of them, system1.ndx and
> system2.ndx, and planned to do something like this:
> echo Protein_ligand1|trjconv -s system1.tpr -f system1.xtc -o
> system1_dehyd.xtc -n system1.ndx
> and, separately, do
> echo Protein_ligand2|trjconv -s system2.tpr -f system2.xtc -o
> system2_dehyd.xtc -n system2.ndx
> Inadvertently, I forgot to change stuff in my second script, giving me a
> command like this
> echo Protein_ligand1|trjconv -s system2.tpr -f system2.xtc -o
> system2_dehyd.xtc -n system1.ndx
> Rather than flipping out and telling me that there isn't anything that
> corresponds to Protein_ligand1 in system2.tpr or system2.xtc, however, it
> gave me system2_dehyd.xtc as if nothing went wrong.  When I pulled
> coordinates from that xtc file, it just used the numbers that corresponded
> to Protein_ligand1 in the system2 files without looking at what it was
> actually pulling.
> Next I tried to break it.  system1 has slightly more atoms than system2,
> and
> so I figured if trjconv just ran out of atoms, it'd throw an error.  Not
> really.  If I did this:
> echo System|trjconv -s system2.tpr -f system2.xtc -o system2_dehyd.xtc -n
> system1.ndx
> All I got was:
> Select a group: Selected 0: 'System'
> Segmentation fault
> Finally, I figured if there was no ndx file, I wouldn't get this problem.
> Not so.  If I did
> echo System|trjconv -s system2.tpr -f system1.xtc -o test.xtc
> This time, I did get the following error:
> -------------------------------------------------------
> Program trjconv, VERSION 4.6
> Source code file:
> /home/sryckbos/Downloads/gromacs-4.6/src/tools/gmx_trjconv.c, line: 1312
> Fatal error:
> Index[33820] 33821 is larger than the number of atoms in the
> trajectory file (33820). There is a mismatch in the contents
> of your -f, -s and/or -n files.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> BUT, if I reversed it,
> echo System|trjconv -s system1.tpr -f system2.xtc -o test2.xtc
> There was no error, and I got test2.xtc out without any problems.
> This seems like a pretty major bug to me, and presumably this isn't
> occurring because I'm not up to date (didn't see anything about it in any
> of
> the release notes for the 4.6.x series, or on any of the mailing lists).
> Has anyone else experienced or noticed this issue?
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/trjconv-doesn-t-check-if-the-tpr-xtc-and-ndx-files-provided-match-tp5014178.html
> Sent from the GROMACS Developers Forum mailing list archive at Nabble.com.
> --
> Gromacs Developers mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_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-developersor send a mail to
> gmx-developers-request at gromacs.org.

Tsjerk A. Wassenaar, Ph.D.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20140131/b8547f8b/attachment-0001.html>

More information about the gromacs.org_gmx-developers mailing list