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: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of sangeeta kundu
Sent: Fri 09/02/2007 10:13 AM
To: gmx-users@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.
regards
SANGEETA
---------------------------------
Here's a new way to find what you're looking for - Yahoo! Answers
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
