[gmx-users] problem regarding do_dssp

sangeeta sangeeta at bic.boseinst.ernet.in
Wed Feb 7 10:41:29 CET 2007

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.


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 
> > 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 
> > than 4 days, yet it was not completed, Only it was giving the 
> > 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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