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

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  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/pdb_lib.py > pdb_lib.py
 
  curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.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
+
   
 
+
     python close_sph.py delphi.sph ../xtal-lig.pdb delphi_close.sph 2.0
 
+
    head delphi_close.sph
  
 +
if there are too mean sphere (> 10,000), decrease the distance.
  
 
Note that this is avalible through the DOCK3.6 release.  
 
Note that this is avalible through the DOCK3.6 release.  

Revision as of 10:20, 3 November 2016

1) Run blastermaster.py. this will gerenate two directorys: working and dockfiles

2) make a new directory called mk_thin_spheres:

  mkdir  mk_thin_spheres
  cd mk_thin_spheres

3 move the molcular surface to the new directory:

  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 (> 10,000), decrease the distance.

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

   blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag