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
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.
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.
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
- parameter scanning.