[gmx-users] a question

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 8 02:44:41 CET 2008

Quoting yc04023 <yc04023 at 163.com>:

>  dear all,
>  i have a question about the do_dssp command, when i use it ,i found it can't
> work out the result after more than one day, it stop in the follow place:
>  There are 42 residues in your selected group
>  Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
>   trn version: GMX_trn_file (single precision)
>   Reading frame       1 time    2.500
>   Back Off! I just backed up ddGPARx0 to ./#ddGPARx0.1#
>  my simulate time is 10ns, and i can use the VMD to see its trajectory, there
> is no abnormal.
>  my command is: do_dssp -s 1_md.tpr -f 1_md.trr -b 1 -e 10000  -o 1_ss.xpm,
> and i select the group----protein.
>  what's wrong with my job?

Use the group 'MainChain'


> I am looking forward to your reply,thanks!
>   greetings,
>   Cao Yang.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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