[gmx-users] problem regarding dssp

[sangeeta]

Dear Tsjerk,
    
     I am sorry I cannot give you the output produced right at the moment 
when the command "do_dssp -s md.tpr -f traj.xtc." was issued, as far as I 
remember for that particular program Gromacs was not producing any 
informative text, as it does in case of other programs, At this moment I do 
not have the  opportunity to access that program due to some internal 
error,so at this very moment I can not reproduce the result.I can assure you 
that  next time I will definitely report you about the output if it produces 
any, and I hope you will help.



regards
SANGEETA    
On Thu, 25 Jan 2007 13:32:26 +0100, Tsjerk Wassenaar wrote
> 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.
> 
> Tsjerk
> 
> 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
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