Re: [gmx-users] dssp error

On 27/03/2012 8:50 PM, Albert wrote: hello: I am trying to run do_dssp by command: do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm but it said: Select a group: 1 Selected 1: 'Protein' There are 35 residues in your selected group trn version: GMX_trn_file (single precision) Reading fr

Re: [gmx-users] dssp error

Hi, I used to have similar problem. Try using double precision. Worked for me. Best Quoting Albert : hello: I am trying to run do_dssp by command: do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm but it said: Select a group: 1 Selected 1: 'Protein' There are 35 residues in your sele

Re: [gmx-users] dssp error

What's your dssp version? The most recent ones have different flags that are not yet supported by gromacs. Erik 27 mar 2012 kl. 11.50 skrev Albert: > hello: > I am trying to run do_dssp by command: > > do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm > > but it said: > > Select a g

Re: [gmx-users] DSSP error

I do not have any problem. The problem is solved. Thank you very much 10 Kasım 2010 22:45 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear Justin, >> >> Finally, The problem is solved, Thank you very much for your patience. >> >> Ps: I set *r...@ab-desktop:/home/ab/Deskto

Re: [gmx-users] DSSP error

ahmet yıldırım wrote: Dear Justin, Finally, The problem is solved, Thank you very much for your patience. Ps: I set *r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp* the instead of 4.step but the do_dssp dont run again.The I don't still understand why the DSSP environ

Re: [gmx-users] DSSP error

Dear Justin, Finally, The problem is solved, Thank you very much for your patience. Ps: I set *r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp* the instead of 4.step but the do_dssp dont run again.The I don't still understand why the DSSP environment variable is not run. T

Re: [gmx-users] DSSP error

ahmet yıldırım wrote: 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp

Re: [gmx-users] DSSP error

1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp Dear Justin, I compiled the p

Re: [gmx-users] DSSP error

May be the directory you are working in is read only, as Justin mentioned this could be a permissions issue. As an example the super computer that I use, cannot write anything in the home directory, therefore all simulations and analysis are done in scratch. Ali -- gmx-users mailing listgmx-

Re: [gmx-users] DSSP error

Justin A. Lemkul wrote: ahmet yıldırım wrote: Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file That seems to indicate that the dssp executable does not match your architecture. Get rid of

Re: [gmx-users] DSSP error

ahmet yıldırım wrote: Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file That seems to indicate that the dssp executable does not match your architecture. Get rid of this executable and compile

Re: [gmx-users] DSSP error

Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file 2010/11/10 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear Justin, I don't undertand you said "you haven't chmod +x dssp)?" >> Please look a

Re: [gmx-users] DSSP error

ahmet yıldırım wrote: Dear Justin, I don't undertand you said "you haven't chmod +x dssp)?" Please look at attached photo? I guess that means it's executable; I'm not used to looking into things with the filesystem browser window. I just couldn't remember if the dssp executable was, by d

Re: [gmx-users] DSSP error

ahmet yıldırım wrote: Hi, Please tell me which step is wrong:( 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# mv dssp /usr/local/bin 4.step-r...@ab-desktop:/home/ab/

Re: [gmx-users] DSSP error

Hi, Please tell me which step is wrong:( 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# mv dssp /usr/local/bin 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=

RE: [gmx-users] DSSP error

http://biskit.pasteur.fr/install/applications/dssp http://oldwww.gromacs.org/pipermail/gmx-users/2009-April/041004.html http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp?highlight=dssp HTH, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...