On 10/13/13 11:56 PM, Mass wrote:
Hi Justin
Here is the copied and pasted output
Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls
-l
-rw--- 1 Mass Mass 15351454992 Aug 21 07:51 bLac_orig_md2.trr
Try giving readable permissions to all, i.e. chmod +r.
Hi Justin
Here is the copied and pasted output
Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$
ls -l
total 92332632
-rw-rw-r-- 1 Mass Mass 0 Sep
8 19:46 310Helix.dat
-rw--- 1 Mass Mass 371878 Aug
21 07:39 3BLG_115XrayWater.top
-rw-rw-r-- 1 Mass
Dear users;
I am trying to run DSSP and have problem, I typed in terminal
do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
Secondary_Structure_analysis_original_dss.xvg -ssdump
and got the following error,
Program do_dssp, VERSION 4.6.3
Source code file:
On 10/12/13 6:08 PM, Mass wrote:
Dear users;
I am trying to run DSSP and have problem, I typed in terminal
do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
Secondary_Structure_analysis_original_dss.xvg -ssdump
and got the following error,
Program do_dssp, VERSION 4.6.3
Source code
On 25/12/2010 11:03 PM, mustafa bilsel wrote:
Hi Justin,
maybe I am making a mistake with installation. What I am doing is this:
I am creating a diretory called DSSP, then I write
rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ http://rsync.cmbi.ru.nl/dssp/
/home/m/DSSP/
on the terminal, and then
http://biskit.pasteur.fr/install/applications/dssp
wget ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip
unzip dsspcmbi.zip
cd dssp
./DsspCompileGCC
cd ..
sudo mv dssp /usr/local/src/
cd /usr/local/bin
sudo ln -s ../src/dssp/dsspcmbi .
lina
On Sat, Dec 25, 2010 at 8:45 PM, Mark
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have caheceked gromacs website
export DSSP=/path/to/dssp
setenv DSSP /path/to/dssp
On Fri, Dec 24, 2010 at 11:38 AM, mustafa bilsel mfbil...@gmail.com wrote:
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have
pawan raghav wrote:
I have download dsspcmbi.zip and extract the dssp folder into
/cygdrive/c/cygwin/usr/local/bin/ directory. Then
set the environment variable export
DSSP=/cygdrive/c/cygwin/usr/local/bin/dssp for bash. then I have gone to
my folder by using cd where all my md files were
Dear all
I want ti install DSSP for visualization of secondary structure in
gromacs analysis.
I am doing following procedure..
Copy the executable dsspcmbi to /usr/bin or /usr/local/bin
ln -s dsspcmbi dssp
And running it for my Pdb like that
dssp file.pdb file.dssp
BUt I am getting error
rituraj purohit wrote:
Dear all
I want ti install DSSP for visualization of secondary structure in
gromacs analysis.
I am doing following procedure..
Copy the executable dsspcmbi to /usr/bin or /usr/local/bin
ln -s dsspcmbi dssp
And running it for my Pdb like that
dssp file.pdb file.dssp
will find out the procedure for
adding ions. Finding out how many ions to add is for you to calculate :-)
Mark
--
Message: 7
Date: Thu, 4 Jun 2009 12:52:32 +0530
From: rituraj purohit riturajpuro...@gmail.com
Subject: [gmx-users] DSSP problem
To: gmx
: [gmx-users] DSSP problem
To: gmx-users@gromacs.org
Message-ID:
685cca3f0906040022j73103651p972ec3922736e...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Dear all
I want ti install DSSP for visualization of secondary structure in
gromacs analysis.
I am
rituraj purohit wrote:
Dear mark
Where i can get the file with permission.
I downloaded from http://swift.cmbi.kun.nl/gv/dssp/
Please do not send copies of entire digests in your emails. That breaks
searches and wastes time and bandwidth.
You give the file permissions in the standard Unix
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