[gmx-users] problem still lies regarding dssp

Naser, Md Abu mn2 at hw.ac.uk
Fri Feb 9 12:04:16 CET 2007

Hi Sangeeta,

Let me ask you few questions in order to solve the problem. 

Are you sure your do_dssp prog were running or it was hanged?
To make sure please try using verbose output using -v option.

Is your computer shared among too many people? 

What is the file permission status of dssp?

To find out use: ls -l /directory/where/you/put/dssp

If you see any restricton to file permission change it to

chmod a+rx dssp

Hope this will help.

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: mn2 at hw.ac.uk
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of sangeeta kundu
Sent: Fri 09/02/2007 10:13 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] problem still lies regarding dssp
Dear All,
            I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not working, or I am making any mistake, but all the other programs of Gromacs like pdb2gmx, editconf , genbox, grompp, mdrun etc are going on successfully, problem lies only in case of dssp, I was suggested by Mark to try dssp independently on a single snapshot extracted from the trajectory,  I took the snapshot of the protein after 500ps  with the command trjconv -f md.xtc -s md.tpr -o time_500ps.pdb -dump 500
  (I think the command is correct, if not I earnestly request you to rectify my mistake), When I ran do_dssp on this single structure I waited for 3 days, but it did not finish and seems to be neverending, then I killed the program, In order to get that particular coloured plot of secondary structure vs time which method should I adopt? Seeking your help and thanks in advance.

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