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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>
<BR>
Your out dose not say that the programme is really running.<BR>
Can you try with .trr and .tpr file and see you get something at<BR>
the bottom of the output like:<BR>
<BR>
Reading frame 0 time 0.000<BR>
Back Off! I just backed up ddQmCBhK to ./#ddQmCBhK.1#<BR>
Reading frame 20 time 40.000<BR>
<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: Mon 12/02/2007 9:55 AM<BR>
To: Discussion list for GROMACS users<BR>
Subject: RE: [gmx-users] problem still lies regarding dssp<BR>
<BR>
Dear Abu and Mark,<BR>
<BR>
You asked me, whether my computer is shared by many, it is not, I think the program was not hanged because while executing do_dssp -v as usual Gromacs output was given,<BR>
<BR>
":-) G R O M A C S (-:<BR>
<BR>
GROningen Mixture of Alchemy and Childrens' Stories<BR>
<BR>
:-) VERSION 3.3.1 (-:<BR>
<BR>
<BR>
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<BR>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<BR>
Copyright (c) 2001-2006, The GROMACS development team,<BR>
check out <A HREF="http://www.gromacs.org">http://www.gromacs.org</A> for more information.<BR>
<BR>
This program is free software; you can redistribute it and/or<BR>
modify it under the terms of the GNU General Public License<BR>
as published by the Free Software Foundation; either version 2<BR>
of the License, or (at your option) any later version.<BR>
<BR>
:-) do_dssp (-:<BR>
<BR>
Option Filename Type Description<BR>
------------------------------------------------------------<BR>
-f traj.xtc Input Generic trajectory: xtc trr trj gro g96 pdb<BR>
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb<BR>
xml<BR>
-n index.ndx Input, Opt. Index file<BR>
-ssdump ssdump.dat Output, Opt. Generic data file<BR>
-map ss.map Input, Lib. File that maps matrix data to colors<BR>
-o ss.xpm Output X PixMap compatible matrix file<BR>
-sc scount.xvg Output xvgr/xmgr file<BR>
-a area.xpm Output, Opt. X PixMap compatible matrix file<BR>
-ta totarea.xvg Output, Opt. xvgr/xmgr file<BR>
-aa averarea.xvg Output, Opt. xvgr/xmgr file<BR>
<BR>
Option Type Value Description<BR>
------------------------------------------------------<BR>
-[no]h bool no Print help info and quit<BR>
-[no]X bool no Use dialog box GUI to edit command line options<BR>
-nice int 19 Set the nicelevel<BR>
-b time 0 First frame (ps) to read from trajectory<BR>
-e time 0 Last frame (ps) to read from trajectory<BR>
-dt time 0 Only use frame when t MOD dt = first time (ps)<BR>
-tu enum ps Time unit: ps, fs, ns, us, ms or s<BR>
-[no]w bool no View output xvg, xpm, eps and pdb files<BR>
-[no]xvgr bool yes Add specific codes (legends etc.) in the output<BR>
xvg files for the xmgrace program<BR>
-sss string HEBT Secondary structures for structure count<BR>
<BR>
"<BR>
<BR>
I changed the permission of dsspcmbi and dsspcmbi.exe files , what else I should do? I mean execpt these two files what are the other files that need change of permission now these two files has read, write, and executable permission, Mark suggested me to call dssp "by hand", will you please explain in more detail?? In order to get taht particular coloured map what procedure should I adopt??<BR>
<BR>
regards<BR>
SANGEETA <BR>
"Naser, Md Abu " <mn2@hw.ac.uk> wrote:<BR>
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>
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