Hello I am sorry for wasting your time. The online GROMACS help is enough to fix my problem.
I am giving it below. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp The problem is fixed now!! Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. On Thu, Jan 29, 2015 at 8:16 PM, Agnivo Gosai <agnivogromac...@gmail.com> wrote: > Dear Users > > I want to calculate the secondary structure stability by using DSSP in > GROMACS 4.6.7. > These are the commands that I used for the same :- > > (1) ./dssp-2.0.4-linux-i386 ( I am running the DSSP executable ) > > (2) source /usr/local/gromacs/bin/GMXRC (sourcing GROMACS from my terminal) > > (3) export DSSP=/home/upamanyu/Desktop/GROMACS (exporting the path to the > DSSP executable , it is located tin the folder GROMACS) > > (4) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc -ver 2 > > I am able to select the group protein at this stage. Then on hitting enter > this error comes. > > Fatal error: > Failed to execute command: Try specifying your dssp version with the -ver > option. > > > (5) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc -ver 1 > > Same error comes > > (6) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc > > Same error comes > > (7) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc -ver 2.0.4 > > Same error comes > > (8) ./dssp-2.0.4-linux-i386 -i pull1.pdb -o pull1.dssp > > This works fine. But I want to use GROMACS to generate plots and figures > with its do_dssp command. > > Kindly help me to find a solution. > > Thanks & Regards > Agnivo Gosai > Grad Student, Iowa State University. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
