Try running with -v option. It might give you clue where is the problem. Abu Naser
School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -----Original Message----- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Mon 05/02/2007 7:56 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] problem regarding do_dssp > > 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
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