Re: [gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)
On Thu, Oct 13, 2011 at 5:16 PM, Ahmad Randy wrote: > Hi All, > > I understand that there were already some discussions about new DSSP exec > with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that > this two DSSP and do_dssp do not compatible each other? > > I was running in Ubuntu 10.04, and this is what I got: > > do_dssp -f 300K.trr -s 300K.tpr -o dssp > > I choose 5 'Mainchain' > > Fatal error: > Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ > ddvDjL4J > /dev/null 2> /dev/null > > > I already set the "export DSSP=/home/madndy/dssp/dssp", and also try the > latest do_dssp.c (from gromacs-4.6) file for instalation. Still didn't work. > > Are there are any suggestion or correction in my step? Or what version of > gromacs that work well with DSSP? Or should I get the older version of DSSP > that work with do_dssp? And where can I find the older version of DSSP > because I can't find the older version in: > http://swift.cmbi.ru.nl/gv/dssp/ . > http://biskit.pasteur.fr/install/applications/dssp You may click above link (untested, be careful). > Thanx, > Randy > > -- > 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 > -- 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] New DSSP vs do_dssp (gromacs-4.5.4)
On 13/10/2011 8:16 PM, Ahmad Randy wrote: Hi All, I understand that there were already some discussions about new DSSP exec with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that this two DSSP and do_dssp do not compatible each other? If the new DSSP requires the code in do_dssp to be updated, that hasn't happened, and likely won't happen for a while. If someone can substantiate that it needs a change, and file a GROMACS Redmine issue describing what needs to happen, then it will be considered for the 4.6 release. I was running in Ubuntu 10.04, and this is what I got: do_dssp -f 300K.trr -s 300K.tpr -o dssp I choose 5 'Mainchain' Fatal error: Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ ddvDjL4J > /dev/null 2> /dev/null I already set the "export DSSP=/home/madndy/dssp/dssp", and also try the latest do_dssp.c (from gromacs-4.6) file for instalation. Still didn't work. Are there are any suggestion or correction in my step? Or what version of gromacs that work well with DSSP? Or should I get the older version of DSSP that work with do_dssp? I think that is the most reliable approach. And where can I find the older version of DSSP because I can't find the older version in: http://swift.cmbi.ru.nl/gv/dssp/ . They say it is available. Please ask them. 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
[gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)
Hi All, I understand that there were already some discussions about new DSSP exec with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that this two DSSP and do_dssp do not compatible each other? I was running in Ubuntu 10.04, and this is what I got: do_dssp -f 300K.trr -s 300K.tpr -o dssp I choose 5 'Mainchain' Fatal error: Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ ddvDjL4J > /dev/null 2> /dev/null I already set the "export DSSP=/home/madndy/dssp/dssp", and also try the latest do_dssp.c (from gromacs-4.6) file for instalation. Still didn't work. Are there are any suggestion or correction in my step? Or what version of gromacs that work well with DSSP? Or should I get the older version of DSSP that work with do_dssp? And where can I find the older version of DSSP because I can't find the older version in: http://swift.cmbi.ru.nl/gv/dssp/ . Thanx, Randy-- 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
