[gmx-users] problem regarding do_dssp

[sangeeta]

Thanks for your suggestion.


regards
Sangeeta

On Wed, 07 Feb 2007 18:17:07 +0800, Yang Ye wrote
> do_dssp calls external dssp program to do the calculation which is 
> slow but shall not take "lot of time" . For fast execution of DSSP,
>  you may consider using my_dssp.
> 
> Go to your gromacs source directory:
> ./configure
> make
> cd src/contrib
> make my_dssp
> 
> Regards,
> Yang Ye
> 
> On 2/7/2007 5:41 PM, sangeeta wrote:
> > Dear Mark, 
> >
> >    Previously you suggested to try running dssp independently on a 
single 
> > snapshot extracted from the trajectory,I took the snapshot of the 
protein 
> > after 1ns with the command 
> >
> > trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000
> >
> > then ran dssp program by using the command 
> >
> > dsspcmbi time_1000ps.pdb DSSPtime_1000ps.pdb 
> >
> >  The program ran successfully,but again when I used 
> >  
> > do_dssp -s md.tpr -f time_1000ps.pdb 
> >   
> > the program is taking lot of time.I do not understand where I am making 
the  
> > mistake, please help and give me solution.Thanks in advance.
> >
> >
> > regards
> > SANGEEA
> >
> > On Mon, 5 Feb 2007 18:56:22 +1100 (EST), Mark Abraham wrote
> >   
> >>> Dear All,
> >>>
> >>>        I want to analyze the secondary structure of a protein after a 
> >>>       
> > 10ns
> >   
> >>> simulation run. Previously I faced difficulty in running dssp 
program,So
> >>> in
> >>> order to  give a test run I ran the do_dssp program  for  100ps
> >>> trajectory
> >>> only for  a protein containing 130 residues.The program continued for 
> >>>       
> > more
> >   
> >>> than 4 days, yet it was not completed, Only it was giving the 
> >>>       
> > intermediate
> >   
> >>> files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were 
produced.I
> >>> do
> >>> not understand how long it will take or whether I am encountering any
> >>> problem , in  the manual it is mentioned that the program is very slow,
> >>> But
> >>> I am not getting any idea whether the time it is taking  is normal, or 
I
> >>> am
> >>> facing some problem.
> >>>       
> >> Try doing it on one structure in a trajectory by using trjconv
> >> appropriately. If it's not done in ten minutes on a machine under 
> >> five years old, then you have a problem.
> >>
> >> Also try running dssp independently on a single snapshot extracted from
> >> your trajeotry and put into pdb format (by specifying .pdb suffix on
> >> output file for trjconv). If you can't do that, then the problem has
> >> nothing to do with gromacs.
> >>
> >> Mark
> >>
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> >
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