Re: [gmx-users] DSSP problem

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. Wit

Re: [gmx-users] DSSP problem

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 M

Re: [gmx-users] DSSP problem

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 file

[gmx-users] DSSP problem

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: /home/mass/gromacs-4.6.3/src/gmxli

Re: [gmx-users] dssp problem

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 Abraham

Re: [gmx-users] dssp problem

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/ /home/m/DSSP/ on the terminal, and the

[gmx-users] dssp problem

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/ /home/m/DSSP/ on the terminal, and then file transfer starts. Then I write export DSSP=/home/m/DSSP/dssp (pointing the ex

Re: [gmx-users] dssp problem

On Fri, Dec 24, 2010 at 11:38 AM, mustafa bilsel 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 caheceked gromacs

[gmx-users] dssp problem

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 command

Re: [gmx-users] dssp problem

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 pre

[gmx-users] dssp problem

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 present i.e. /cygdrive/c/grom

Re: [gmx-users] DSSP problem

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

Re: [gmx-users] DSSP problem

strength > > To: gmx-users@gromacs.org > > Message-ID: <418624.33836...@web8708.mail.in.yahoo.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear gromacs users, > > > > I am simulating a protein which works in salt solu

[gmx-users] DSSP problem

n advance. > Amrita Paul > > > > > Cricket on your mind? Visit the ultimate cricket website. Enter > http://beta.cricket.yahoo.com > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20

Re: [gmx-users] DSSP problem

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

[gmx-users] DSSP problem

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