But right now I noticed something a bit funny, Try different times,
Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1# ------------------------------------------------------- Program do_dssp, VERSION 4.0.7 Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy > /dev/null 2> /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz > /dev/null 2> /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax > /dev/null 2> /dev/null Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k > /dev/null 2> /dev/null was something wrong with mine DSSP, except path reason. Thanks, lina ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Friday, November 05, 2010 9:35 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] dssp Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the "real and true" path to a simple way as it showed "pathTo..." before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp Linus Östberg wrote: > What did you try to do? To use dssp, you must select entire residues, > e.g. 1 (protein). That error sounds a bit like my problem when trying > to do dssp using only the backbone. > The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing "dssp," do_dssp was executing "pathToDSSP" instead. The group for analysis is also debatable. I have seen hangs and seg faults when "Protein" is selected, and other times it works fine. The only absolute requirement is that (at least) all "MainChain" atoms be considered. The latest version of GROMACS seems to handle "Protein" just fine, but older versions did not. I have no explanation for that, however :) -Justin > // Linus Östberg > > On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# <zhao0...@e.ntu.edu.sg> wrote: >> Hi, >> >> Thanks for your response, I modified that path parts when I posted that >> information. >> >> So my environment set was correct. >> >> I just suddenly realize I may not have root privilege there, cause the dssp >> was not small, not in mine personal computer, there are in some other places. >> >> lina >> >> ________________________________________ >> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on >> behalf of Justin A. Lemkul [jalem...@vt.edu] >> Sent: Friday, November 05, 2010 9:07 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] dssp >> >> #ZHAO LINA# wrote: >>> Hi, >>> >>> Program do_dssp, VERSION 4.0.7 >>> Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 >>> >>> Fatal error: >>> Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz > /dev/null >>> 2> /dev/null >>> >>> It came out two or three file like ddEPI6I2 and then died like above. >>> >>> My first time try dssp, so do not know how to examine it. >>> >> Your DSSP environment variable is set incorrectly. do_dssp is trying to call >> "pathToDSSP" as the executable. >> >> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp >> >> Note that you should substitute a meaningful PATH on your system, not >> something >> like "pathToDSSP." >> >> -Justin >> >>> Thanks for any advice, >>> >>> lina >>> >> -- >> ======================================== >> >> 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 list 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. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list 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. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- ======================================== 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 list 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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists