[gmx-users] question about dssp

[David van der Spoel]

On Thu, 2005-11-10 at 19:24 +0800, Wang Zhun wrote:
> 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?
Try selecting protein, maybe it gets confused by only having the C-alpha
atoms.
> 
> 
> Thanks.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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