Using thin spheres in DOCK3.7

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Tutorial for using Thin Spheres in DOCK 3.7

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

1) Run 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/ .
  $DOCKBASE/proteins/dms/bin/dms rec.pdb -a -d 0.2 -i -g dms.log -p -n -o

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/ .

4) Run the thin spheres code:

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

or an updated version is located here:

/mnt/nfs/home/tbalius/zzz.github/DOCK/proteins/thinspheres/ -i -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. will soon be included with DOCK3.7.

Get the following python code:

curl >
curl >
curl >
   python 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.

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

   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/ --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/ --useExistingLowDielectricSphflag --addNOhydrogensflag --radiusFile=/present/working/directory/vdw.siz -v

8) optional.

  • parameter scanning.

how to do parameter scanning