[gmx-users] problem still lies regarding dssp
sangeeta kundu
sangeeta0983 at yahoo.co.in
Tue Feb 13 05:44:52 CET 2007
"Naser, Md Abu " <mn2 at hw.ac.uk> wrote: Yes Abu,
I have seen it, while executing do_dssp with the .xtc file I have seen those commands.
regards
SANGEETA
Hi Sangeeta,
Your out dose not say that the programme is really running.
Can you try with .trr and .tpr file and see you get something at
the bottom of the output like:
Reading frame 0 time 0.000
Back Off! I just backed up ddQmCBhK to ./#ddQmCBhK.1#
Reading frame 20 time 40.000
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: Mon 12/02/2007 9:55 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] problem still lies regarding dssp
Dear Abu and Mark,
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,
":-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) do_dssp (-:
Option Filename Type Description
------------------------------------------------------------
-f traj.xtc Input Generic trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
xml
-n index.ndx Input, Opt. Index file
-ssdump ssdump.dat Output, Opt. Generic data file
-map ss.map Input, Lib. File that maps matrix data to colors
-o ss.xpm Output X PixMap compatible matrix file
-sc scount.xvg Output xvgr/xmgr file
-a area.xpm Output, Opt. X PixMap compatible matrix file
-ta totarea.xvg Output, Opt. xvgr/xmgr file
-aa averarea.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-sss string HEBT Secondary structures for structure count
"
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??
regards
SANGEETA
"Naser, Md Abu " <mn2 at hw.ac.uk> wrote:
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.
regards
SANGEETA
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