[gmx-users] problem regarding do_dssp

[Mark Abraham]

>
> 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