[gmx-users] problem regarding dssp

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 25 13:32:26 CET 2007

Hi Sangeeta,

My request was actually for the text which do_dssp output to the
screen. At this point I do not intend to try to reproduce your error,
and the intermediate files will not prove useful anyway. Running any
of the gromacs programs gives plenty of informative text thrown out to
the screen, in particular when things go wrong. I'm sorry if I haven't
been clear enough there.


On 1/25/07, sangeeta <sangeeta at bic.boseinst.ernet.in> wrote:
> Dear Tsjerk,
>       Previously I send you the intermediate files which are the output of
> DSSP,as per your request, I think I should submit the input files also, so
> here I am attaching the .mdp and .xtc files, the command I used was
> do_dssp -s md.tpr -f traj.xtc.I want to get the particular type of plot of
> secondary structural elements over time as stated in the manual.I
> downloaded  DSSP from the link
> http://swift.cmbi.ru.nl/gv/dssp/
> and according to the instruction unpacked by using the command  "unzip
> dsspcmbi.zip  ", the dssp program by itself ran successfully with the typed
> command
> "dsspcmbi PDBSourcefile DSSPDestinationfile  ", and I could view the
> destination file with all the structural informations. But when I tried to
> correlate with Gromacs by using  "do_dssp -s md.tpr -f traj.xtc" the
> intermediate files are only produced.I understand that something is going
> wrong but can not detect it, please help.Thanks in advence.
> regards
> Sangeeta Kundu
> Junior Research Fellow
> Bose Institute, Kolkata
> India
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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

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