[gmx-users] question about dssp

[Marco Pasi]

Dear Wang,

I have been experiencing the same problem today for the first time,
after using do_dssp successfully in the last days.  I solved my
problem by setting an environmental variable DSSP as the path of the
dsspcmbi executable (in bash):

export DSSP=/usr/local/bin/dssp/dsspcmbi

This was enough for me, hope it's useful for you.
Bye

Marco Pasi

On 11/10/05, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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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