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

[gmx-users] dssp error

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 frame 400 time 400.000 Back Off! I j

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

edo...@gmail.com <mailto:ahmedo...@gmail.com> <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>>>] *Sent:* Wednesday, November 10, 2010 10:02 PM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] DSSP erro

Re: [gmx-users] DSSP error

...@gmail.com <mailto:ahmedo...@gmail.com> <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>> <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com> <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>>>]

Re: [gmx-users] DSSP error

oun...@gromacs.org >><mailto:gmx-users-boun...@gromacs.org> >> <mailto:gmx-users-boun...@gromacs.org >><mailto:gmx-users-boun...@gromacs.org>> >> >> [gmx-users-boun...@gromacs.org >><mailto:gmx-users-

Re: [gmx-users] DSSP error

<mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>>] *Sent:* Wednesday, November 10, 2010 10:02 PM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] DSSP error Hi, I installed in /usr/local/bin the DSSP program. And I s

Re: [gmx-users] DSSP error

ember 10, 2010 10:02 PM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] DSSP error Hi, I installed in /usr/local/bin the DSSP program. And I set the environment variable with a command such as “export DSSP=/usr/local/bin/dssp”. a...@ubuntu:/Desktop/work#

Re: [gmx-users] DSSP error

t=dssp > > HTH, > > lina > -- > *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of ahmet yıldırım [ahmedo...@gmail.com] > *Sent:* Wednesday, November 10, 2010 10:02 PM > *To:* Discussion list for GROMACS users > *Subject:* [gmx-us

RE: [gmx-users] DSSP error

...@gromacs.org] on behalf of ahmet yıldırım [ahmedo...@gmail.com] Sent: Wednesday, November 10, 2010 10:02 PM To: Discussion list for GROMACS users Subject: [gmx-users] DSSP error Hi, I installed in /usr/local/bin the DSSP program. And I set the environment variable with a command such as “export

[gmx-users] DSSP error

Hi, I installed in /usr/local/bin the DSSP program. And I set the environment variable with a command such as “export DSSP=/usr/local/bin/dssp”. a...@ubuntu:/Desktop/work# do_dssp -s run.tpr -f run.xtc ... Selected 1: 'Protein' There are 164 residues in your selected group Opening library file /us