[Dock-fans] problem with dms:

Scott Brozell sbrozell at scripps.edu
Thu Jul 26 15:13:45 PDT 2007


Hi,

On Tue, 24 Jul 2007, Parminder Mankoo wrote:

> I am trying to learn DOCK6 to dock atp into a kinase. I am following the
> tutorials and now stuck at the step where I need
> _____________________
> ../dms/bin/dms atp.pdb -n -w 1.4 -v -o atp.ms
>
> No atoms in input file!
> ________________________
>
> The atp.pdb file is not empty. It is as following:
> EXPDTA    THEORETICAL MODEL, MODELLER SVN 2007/07/16 21:23:51
> ATOM      1  PG  ATP  1391      28.876  68.006  19.624  1.00 92.35
> P
> ATOM      2  O3B ATP  1391      27.839  66.717  19.158  1.00 91.75
> O
...

dms/man/man1/dms.1

       -a     Include all atoms, not just those in amino acid and nucleic acid
              residues.

Also be careful with the PDB format
http://www.wwpdb.org/documentation/format23/sect9.html

EXPDTA    THEORETICAL MODEL, MODELLER SVN 2007/07/16 21:23:51
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM      1  PG  ATP  1391      28.876  68.006  19.624  1.00 92.35           P
ATOM      2  O3B ATP  1391      27.839  66.717  19.158  1.00 91.75           O
ATOM      3  PB  ATP  1391      27.136  66.147  17.708  1.00 89.86           P
ATOM      4  O3A ATP  1391      25.700  65.646  18.125  1.00 89.34           O
ATOM      5  PA  ATP  1391      24.999  64.238  18.558  1.00 88.85           P
ATOM      6  O5' ATP  1391      23.527  64.665  18.713  1.00 86.03           O
ATOM      7  C5' ATP  1391      23.084  65.460  19.796  1.00 84.42           C
ATOM      8  C4' ATP  1391      21.636  65.673  19.598  1.00 80.99           C

../dms/bin/dms atp.pdb -a -n -w 1.4 -v -o atp.ms
8 atoms
        P       3
        O       3
        C       2
Servers initialized
Neighbors computed
Probes computed
Neighbors sent
Surface computed
Server request count:
        localhost       79
862 points      (569 contact, 293 reentrant)
161.65 sq. A    (112.40 contact, 49.25 reentrant)
5.33 pts/sq.A   (5.06 contact, 5.95 reentrant)

Scott



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