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

Ragnarok sdf fabracht1 at gmail.com
Tue Sep 30 17:02:51 CEST 2008

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080930/f7e48f08/attachment.html>

More information about the gromacs.org_gmx-users mailing list