Using thin spheres in DOCK3.7

Tutorial for using Thin Spheres in DOCK 3.7

Written by Trent E. Balius, 2016/11/03.

1) Run blastermaster.py. This will generate two directories: working and dockfiles

2) Make a new directory called mk_thin_spheres:

  mkdir  mk_thin_spheres
  cd mk_thin_spheres

3) First lets make a molecular surface. We recommend that you make a less dense molecular surface by copying the rec.pdb and running the following command:

  cp ../rec.pdb .
  cp ../working/rec.site.dms .
  $DOCKBASE/proteins/dms/bin/dms rec.pdb -a -d 0.2 -i rec.site.dms -g dms.log -p -n -o rec.ms

Here, the -d flag allows us to pass the program a scalar to modify the density of the surface points. For example, with a -d set to 1.0 the density is will be 5.42 pts/sq.A, while with a -d 0.2, we will get a density of 1.18 pts/sq.A.

Instead, you could copy the molecular surface of the original surface (this is OK for small sites):

  cp ../working/rec.ms .

4) Run the thin spheres code:

/mnt/nfs/home/tbalius/zzz.svn/dockenv/trunk/etc/thin_spheres.py -i rec.ms -o delphi.sph >& thin_spheres.log

Note that this is available through the DOCK3.6 release.

or an updated version is located here:

/mnt/nfs/home/tbalius/zzz.github/DOCK/proteins/thinspheres/thin_spheres.py -i rec.ms -o delphi.sph -d 2.0 -s 1.0 >& thin_spheres.log

the -s flag specifies the size (radius) of the sphere and the -d flag, the distance to the surface.

thin_spheres.py will soon be included with DOCK3.7.

Get the following python code:

curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py
   
   python close_sph.py delphi.sph ../xtal-lig.pdb delphi_close.sph 4.0
   head delphi_close.sph

if there are too many spheres (> 1,000), decrease the distance to, say, 1.2.

   cd ../
    move back to the top directory.

5) Now lets setup a directory and files to run blastermaster with the Existing Low Dielectric Spheres make a new directory call dockprep_w_thin_sph/

   mkdir  dockprep_w_thin_sph
   cd dockprep_w_thin_sph
   cp ../rec.pdb ../xtal-lig.pdb .
   mkdir working
   cp ../working/rec.crg.pdb working/
   cp ../mk_thin_spheres/delphi_close.sph working/lowdielectric.sph    

Make sure the header of the sphere file is cluster 1.

   head working/lowdielectric.sph

If it is not and says cluster 0 then run the following, because blaster master expects this to be cluster 1.

   sed -i 's/cluster     0/cluster     1/g' working/lowdielectric.sph

6) Now lets run blastermaster with Existing Low Dielectric Spheres

   $DOCKBASE/proteins/blastermaster/blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag

7) To apply a different radius to the spheres during QNIFFT calculation do the following:

• Copy file to the present working directory.

   cp $DOCKBASE/proteins/defaults/vdw.siz .

• edit the file to change the radius form 1.90 to 1.00:

   sed 's/c     sph   1.90/c     sph   1.00/g'

• run blastermaster including the full path to radiusFile to use the alternative radii (the path may become truncated if too long, this is fix in later version).

   python $DOCKBASE/proteins/blastermaster/blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag --radiusFile=/present/working/directory/vdw.siz -v

8) optional.

• parameter scanning.

how to do parameter scanning