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 " <[EMAIL PROTECTED]> 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: [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: [email protected]
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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