[gmx-users] a question

[Mark Abraham]

yc04023 wrote:
>  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?

See http://wiki.gromacs.org/index.php/do_dssp

Mark