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<P><FONT SIZE=2>Try running with -v option. It might give you clue where is the problem.<BR>
<BR>
Abu Naser<BR>
<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Fax : +44(0) 131 451 3009<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Mark Abraham<BR>
Sent: Mon 05/02/2007 7:56 AM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] problem regarding do_dssp<BR>
<BR>
><BR>
> Dear All,<BR>
><BR>
> I want to analyze the secondary structure of a protein after a 10ns<BR>
> simulation run. Previously I faced difficulty in running dssp program,So<BR>
> in<BR>
> order to give a test run I ran the do_dssp program for 100ps<BR>
> trajectory<BR>
> only for a protein containing 130 residues.The program continued for more<BR>
> than 4 days, yet it was not completed, Only it was giving the intermediate<BR>
> files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I<BR>
> do<BR>
> not understand how long it will take or whether I am encountering any<BR>
> problem , in the manual it is mentioned that the program is very slow,<BR>
> But<BR>
> I am not getting any idea whether the time it is taking is normal, or I<BR>
> am<BR>
> facing some problem.<BR>
<BR>
Try doing it on one structure in a trajectory by using trjconv<BR>
appropriately. If it's not done in ten minutes on a machine under five<BR>
years old, then you have a problem.<BR>
<BR>
Also try running dssp independently on a single snapshot extracted from<BR>
your trajeotry and put into pdb format (by specifying .pdb suffix on<BR>
output file for trjconv). If you can't do that, then the problem has<BR>
nothing to do with gromacs.<BR>
<BR>
Mark<BR>
<BR>
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