Difference between revisions of "Using thin spheres in DOCK3.7"

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3) First lets make a molecular surface.  We recommend that you make a less dense molecular surface by coping the rec.pdb and running the following command:
 
3) First lets make a molecular surface.  We recommend that you make a less dense molecular surface by coping the rec.pdb and running the following command:
 +
  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
 
   $DOCKBASE/proteins/dms/bin/dms rec.pdb -a -d 0.2 -i rec.site.dms -g dms.log -p -n -o rec.ms
  

Revision as of 11:51, 3 November 2016

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 coping the rec.pdb and running the following command:

  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 scaler to modify the density of the surface points. for example, with a -d 1.0 the density is 5.42 pts/sq.A while -d 0.2 we get a density of 1.18 pts/sq.A

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

  cp ../working/rec.ms .

4) run thin sphere code:

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

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 2.0
   head delphi_close.sph

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

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

cd ../ move back to the top dir.

5) now lets setup dir and files to run blastermaster with 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    
   # blaster master expect 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