Hi, Since the release of 4.5.5, DSSP totally changed its command-line interface. So old GROMACS code cannot work with new DSSP. You need to get the old version of DSSP to use with old GROMACS, or new GROMACS code to work with either DSSP.
Mark On Thu, Oct 10, 2013 at 1:37 PM, Mass <masstransfer_2...@yahoo.com> wrote: > Dear Gromacs users, > I have asked this questions before and Justin gave some answers which I > could solve my problem based on his answer. I am using Ubuntu 12.10 and > installed gromacs 4.5.5-2. > this is what I have done > 2- I moved this file to usr/local/bin > 1- first I downloaded the dssp > wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64-O~/dssp > 2- I moved this file to usr/local/bin > > then I run do_dssp and I was asked to select a group > Select a group: 1 > Selected 1: 'Protein' > There are 162 residues in your selected group > trn version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 > Back Off! I just backed up ddQ0FCUF to ./#ddQ0FCUF.1# > > after that I am getting > Program do_dssp, VERSION 4.5.5 > Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: > 572 > > Fatal error: > Failed to execute command: /usr/local/bin/dssp -na ddQ0FCUF ddzUlAvc > > /dev/null 2> /dev/null > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > I really appreciate if anyone can tell me simple and step-by step solution > (I am a beginner user). > > Thanks > > -- > 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
