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 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 just backed up ddbXn2WY to ./#ddbXn2WY.1# --- Program do_dssp, VERSION 4.5.5 Source code file: do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddbXn2WY ddeWknkk /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It's just the way this stuff is done (Built to Spill) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dssp error
Hi, I used to have similar problem. Try using double precision. Worked for me. Best Quoting Albert mailmd2...@gmail.com: 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 just backed up ddbXn2WY to ./#ddbXn2WY.1# --- Program do_dssp, VERSION 4.5.5 Source code file: do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddbXn2WY ddeWknkk /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It's just the way this stuff is done (Built to Spill) Rohit Arora Laboratoire de Biologie et de Pharmacologie Génétique Appliquée (CNRS UMR 8113) Ecole Normale Supérieure, Cachan France Bureau: +33 (0) 1 47 40 77 49 Portable: +33 (0) 6 23 85 12 46 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 frame 400 time 400.000 Back Off! I just backed up ddbXn2WY to ./#ddbXn2WY.1# --- Program do_dssp, VERSION 4.5.5 Source code file: do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddbXn2WY ddeWknkk /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sounds like you haven't followed the instructions in do_dssp -h carefully enough. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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...@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 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 /usr/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up dduigjCp to ./#dduigjCp.1# --- Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null --- Jesus Not Only Saves, He Also Frequently Makes Backups. (Myron Bradshaw) What should I do? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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=/usr/local/bin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp. c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null 10 Kasım 2010 16:08 tarihinde #ZHAO LINA# zhao0...@e.ntu.edu.sg yazdı: 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...@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 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 /usr/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up dduigjCp to ./#dduigjCp.1# --- Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp.c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null --- Jesus Not Only Saves, He Also Frequently Makes Backups. (Myron Bradshaw) What should I do? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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/Desktop/dssp# export DSSP=/usr/local/bin Your environment variable is wrong. Please read about the proper way to set it: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Although, if you've got dssp in /usr/local/bin, that's the default location where do_dssp expects it, so there is no need to set the DSSP environment variable at all. Perhaps your issue is permission? Or you the dssp executable isn't actually executable (i.e., you haven't chmod +x dssp)? -Justin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp. c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null 10 Kasım 2010 16:08 tarihinde #ZHAO LINA# zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg yazdı: 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 mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [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 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 /usr/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up dduigjCp to ./#dduigjCp.1# --- Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp.c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null --- Jesus Not Only Saves, He Also Frequently Makes Backups. (Myron Bradshaw) What should I do? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 default, capable of being executed. The command in the terminal would be what I quoted before. Do a test: can you run the dssp executable on a .pdb file? That is, don't call it via do_dssp, try to use it in its standalone capacity. -Justin Thanks 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu 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/Desktop/dssp# export DSSP=/usr/local/bin Your environment variable is wrong. Please read about the proper way to set it: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Although, if you've got dssp in /usr/local/bin, that's the default location where do_dssp expects it, so there is no need to set the DSSP environment variable at all. Perhaps your issue is permission? Or you the dssp executable isn't actually executable (i.e., you haven't chmod +x dssp)? -Justin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp. c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null 10 Kasım 2010 16:08 tarihinde #ZHAO LINA# zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg yazdı: 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 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-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [ahmedo...@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 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 /usr/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up dduigjCp to ./#dduigjCp.1# --- Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp.c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null --- Jesus Not Only Saves, He Also Frequently Makes Backups. (Myron Bradshaw) What should I do? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM --
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 jalem...@vt.edu 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 default, capable of being executed. The command in the terminal would be what I quoted before. Do a test: can you run the dssp executable on a .pdb file? That is, don't call it via do_dssp, try to use it in its standalone capacity. -Justin Thanks 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu 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/Desktop/dssp# export DSSP=/usr/local/bin Your environment variable is wrong. Please read about the proper way to set it: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Although, if you've got dssp in /usr/local/bin, that's the default location where do_dssp expects it, so there is no need to set the DSSP environment variable at all. Perhaps your issue is permission? Or you the dssp executable isn't actually executable (i.e., you haven't chmod +x dssp)? -Justin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp. c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null 10 Kasım 2010 16:08 tarihinde #ZHAO LINA# zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg yazdı: 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 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-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [ahmedo...@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 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 /usr/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up dduigjCp to ./#dduigjCp.1# --- Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp.c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null --- Jesus Not Only Saves, He Also Frequently Makes Backups. (Myron Bradshaw) What should I do? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org
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 this executable and compile it from source, which I believe is provided when you download dssp. ...or check whether or not dssp is actually executable, as I suggested twice before. -Justin -Justin 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu 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 default, capable of being executed. The command in the terminal would be what I quoted before. Do a test: can you run the dssp executable on a .pdb file? That is, don't call it via do_dssp, try to use it in its standalone capacity. -Justin Thanks 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu 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/Desktop/dssp# export DSSP=/usr/local/bin Your environment variable is wrong. Please read about the proper way to set it: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Although, if you've got dssp in /usr/local/bin, that's the default location where do_dssp expects it, so there is no need to set the DSSP environment variable at all. Perhaps your issue is permission? Or you the dssp executable isn't actually executable (i.e., you haven't chmod +x dssp)? -Justin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp. c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null 10 Kasım 2010 16:08 tarihinde #ZHAO LINA# zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg yazdı: 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 mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@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-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [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 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 set the environment variable with a command such
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 it from source, which I believe is provided when you download dssp. -Justin 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu 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 default, capable of being executed. The command in the terminal would be what I quoted before. Do a test: can you run the dssp executable on a .pdb file? That is, don't call it via do_dssp, try to use it in its standalone capacity. -Justin Thanks 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu 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/Desktop/dssp# export DSSP=/usr/local/bin Your environment variable is wrong. Please read about the proper way to set it: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Although, if you've got dssp in /usr/local/bin, that's the default location where do_dssp expects it, so there is no need to set the DSSP environment variable at all. Perhaps your issue is permission? Or you the dssp executable isn't actually executable (i.e., you haven't chmod +x dssp)? -Justin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp. c, line: 471 *Fatal error:* Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null 10 Kasım 2010 16:08 tarihinde #ZHAO LINA# zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg mailto:zhao0...@e.ntu.edu.sg yazdı: 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 mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@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-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [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 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 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
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-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 program. you said Your environment variable is wrong, Now is it true?? Thanks for your helps 2010/11/10 Ali Naqvi mna...@ryerson.ca 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-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 Dear Justin, I compiled the program. you said Your environment variable is wrong, Now is it true?? Yes, although it's still not necessary. As I said before, if your dssp binary is in /usr/local/bin/dssp, then that's what Gromacs expects. You only have to set the DSSP environment variable if you've got the dssp binary somewhere else. -Justin Thanks for your helps 2010/11/10 Ali Naqvi mna...@ryerson.ca mailto:mna...@ryerson.ca 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-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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. Thanks again Final solution: 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# mv dssp /usr/local/bin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Selected 1: 'Protein' There are 164 residues in your selected group Opening library file /usr/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddqL3oYP to ./#ddqL3oYP.1# Last frame 50 time 10.000 100% gcq#29: No One Could Foresee the End That Came So Fast (Slayer) 2010/11/10 Justin A. Lemkul jalem...@vt.edu 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 Dear Justin, I compiled the program. you said Your environment variable is wrong, Now is it true?? Yes, although it's still not necessary. As I said before, if your dssp binary is in /usr/local/bin/dssp, then that's what Gromacs expects. You only have to set the DSSP environment variable if you've got the dssp binary somewhere else. -Justin Thanks for your helps 2010/11/10 Ali Naqvi mna...@ryerson.ca mailto:mna...@ryerson.ca 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-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 environment variable is not run. I'm confused. You say the problem is solved, then you say that do_dssp is not running, but then your output below indicates that everything is fine. If there is still a problem, please list all your commands in exact order (not this instead of that). To eliminate any sort of confusion, please stop setting the DSSP environment variable if your dssp binary is in /usr/local/bin. As I keep telling you, if this is its location, it is exactly what Gromacs expects and you do not need it whatsoever. You only need to set DSSP if your binary is in some other location. -Justin Thanks again Final solution: 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# mv dssp /usr/local/bin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Selected 1: 'Protein' There are 164 residues in your selected group Opening library file /usr/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddqL3oYP to ./#ddqL3oYP.1# Last frame 50 time 10.000 100% gcq#29: No One Could Foresee the End That Came So Fast (Slayer) 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu 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 Dear Justin, I compiled the program. you said Your environment variable is wrong, Now is it true?? Yes, although it's still not necessary. As I said before, if your dssp binary is in /usr/local/bin/dssp, then that's what Gromacs expects. You only have to set the DSSP environment variable if you've got the dssp binary somewhere else. -Justin Thanks for your helps 2010/11/10 Ali Naqvi mna...@ryerson.ca mailto:mna...@ryerson.ca mailto:mna...@ryerson.ca mailto:mna...@ryerson.ca 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-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
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 jalem...@vt.edu 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/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. I'm confused. You say the problem is solved, then you say that do_dssp is not running, but then your output below indicates that everything is fine. If there is still a problem, please list all your commands in exact order (not this instead of that). To eliminate any sort of confusion, please stop setting the DSSP environment variable if your dssp binary is in /usr/local/bin. As I keep telling you, if this is its location, it is exactly what Gromacs expects and you do not need it whatsoever. You only need to set DSSP if your binary is in some other location. -Justin Thanks again Final solution: 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# mv dssp /usr/local/bin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Selected 1: 'Protein' There are 164 residues in your selected group Opening library file /usr/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddqL3oYP to ./#ddqL3oYP.1# Last frame 50 time 10.000 100% gcq#29: No One Could Foresee the End That Came So Fast (Slayer) 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu 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 Dear Justin, I compiled the program. you said Your environment variable is wrong, Now is it true?? Yes, although it's still not necessary. As I said before, if your dssp binary is in /usr/local/bin/dssp, then that's what Gromacs expects. You only have to set the DSSP environment variable if you've got the dssp binary somewhere else. -Justin Thanks for your helps 2010/11/10 Ali Naqvi mna...@ryerson.ca mailto:mna...@ryerson.ca mailto:mna...@ryerson.ca mailto:mna...@ryerson.ca 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-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
