[gmx-users] help extracting .pdb frame out of run

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Sep 30 19:40:43 CEST 2008

Hi Fabricio,

You can also sue the option -dump 10000 to extract a frame. But it's
not related to your error.
Have you done any fitting and pbc related stuff or did you
shuffle/sort your system prior to running?



On Tue, Sep 30, 2008 at 5:02 PM, Ragnarok sdf <fabracht1 at gmail.com> wrote:
> Hello,
> I have ran a simulation with gromac but can't seem to be able to extract a
> single structure of a determined frame from my .trr file. I wish to obtain a
> pdb file good for reading in CHIMERA, for example.
> I tryed the following command:
> trjconv -f sim.trr -s trjtop.tpr -o pdbiwant.pdb -b 10000 -e 10000.
> Some programs, spdbv, for example, completely mess up my structure, making
> bonds where it shouldn't etc etc. CHIMERA simply cannot find any coordinates
> in the file. But the .pdb generated from trjconv looks ok. I mean , there
> are coordinates and all.
> Any suggestions?
> Thank you in advance
> Fabrício Bracht
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

More information about the gromacs.org_gmx-users mailing list