Dear Mark, Previously you suggested to try running dssp independently on a single snapshot extracted from the trajectory,I took the snapshot of the protein after 1ns with the command
trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000 then ran dssp program by using the command dsspcmbi time_1000ps.pdb DSSPtime_1000ps.pdb The program ran successfully,but again when I used do_dssp -s md.tpr -f time_1000ps.pdb the program is taking lot of time.I do not understand where I am making the mistake, please help and give me solution.Thanks in advance. regards SANGEEA On Mon, 5 Feb 2007 18:56:22 +1100 (EST), Mark Abraham wrote > > > > Dear All, > > > > I want to analyze the secondary structure of a protein after a 10ns > > simulation run. Previously I faced difficulty in running dssp program,So > > in > > order to give a test run I ran the do_dssp program for 100ps > > trajectory > > only for a protein containing 130 residues.The program continued for more > > than 4 days, yet it was not completed, Only it was giving the intermediate > > files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I > > do > > not understand how long it will take or whether I am encountering any > > problem , in the manual it is mentioned that the program is very slow, > > But > > I am not getting any idea whether the time it is taking is normal, or I > > am > > facing some problem. > > Try doing it on one structure in a trajectory by using trjconv > appropriately. If it's not done in ten minutes on a machine under > five years old, then you have a problem. > > Also try running dssp independently on a single snapshot extracted from > your trajeotry and put into pdb format (by specifying .pdb suffix on > output file for trjconv). If you can't do that, then the problem has > nothing to do with gromacs. > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php