[gmx-users] question about dssp

Wang Zhun wangzhun at pumc.edu.cn
Thu Nov 10 12:24:39 CET 2005

Hi, everyone,

There's a strange problem about do_dssp in my Gromacs3.2.1:
The binary DSSP was downloaded from http://swift.cmbi.ru.nl and moved to /usr/local/bin.
I can carry out DSSP to calculate the secondary structure of the pdb file generated by ngmx, but when I carried out do_dssp, it says:

Reading file topol.tpr, VERSION 3.2.1 (single precision)
Reading file topol.tpr, VERSION 3.2.1 (single precision)
Opening library file /usr/local/gromacs/share/top/phbres.dat
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Group     0 (      System) has   239 elements
Group     1 (     Protein) has   239 elements
Group     2 (   Protein-H) has   183 elements
Group     3 (     C-alpha) has    24 elements
Group     4 (    Backbone) has    72 elements
Group     5 (   MainChain) has    97 elements
Group     6 (MainChain+Cb) has   117 elements
Group     7 ( MainChain+H) has   122 elements
Group     8 (   SideChain) has   117 elements
Group     9 ( SideChain-H) has    86 elements
Select a group: 3
Selected 3: 'C-alpha'
There are 24 residues in your selected group
Opening library file /usr/local/gromacs/share/top/ss.map
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
Back Off! I just backed up ddpHemqS to ./#ddpHemqS.1#

And the program stops at this stage. I don't know if it's the do_dssp goes wrong or it's due to the size of traj.trr.
Is the do_dssp a time-consuming process?


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