Thanks for your suggestion.
regards Sangeeta On Wed, 07 Feb 2007 18:17:07 +0800, Yang Ye wrote > do_dssp calls external dssp program to do the calculation which is > slow but shall not take "lot of time" . For fast execution of DSSP, > you may consider using my_dssp. > > Go to your gromacs source directory: > ./configure > make > cd src/contrib > make my_dssp > > Regards, > Yang Ye > > On 2/7/2007 5:41 PM, sangeeta wrote: > > 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 [email protected] > >> 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 [email protected] > > 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 > > > > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected] 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
