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<TITLE>RE: [gmx-users] problem still lies regarding dssp</TITLE>
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<P><FONT SIZE=2>Hi Sangeeta,<BR>
<BR>
Let me ask you few questions in order to solve the problem.<BR>
<BR>
Are you sure your do_dssp prog were running or it was hanged?<BR>
To make sure please try using verbose output using -v option.<BR>
<BR>
Is your computer shared among too many people?<BR>
<BR>
What is the file permission status of dssp?<BR>
<BR>
To find out use: ls -l /directory/where/you/put/dssp<BR>
<BR>
If you see any restricton to file permission change it to<BR>
<BR>
chmod a+rx dssp<BR>
<BR>
Hope this will help.<BR>
<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 sangeeta kundu<BR>
Sent: Fri 09/02/2007 10:13 AM<BR>
To: gmx-users@gromacs.org<BR>
Subject: [gmx-users] problem still lies regarding dssp<BR>
<BR>
Dear All,<BR>
<BR>
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<BR>
(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.<BR>
<BR>
regards<BR>
SANGEETA<BR>
<BR>
<BR>
<BR>
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