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

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Line 22: Line 22:
 
     cp ../rec.pdb ../xtal-lig.pdb .
 
     cp ../rec.pdb ../xtal-lig.pdb .
 
     mkdir working
 
     mkdir working
        cp ../../working/rec.crg.pdb working/.
+
    cp ../../working/rec.crg.pdb working/.
 
     cp ../mk_thin_spheres/delphi.sph working/lowdielectric.sph
 
     cp ../mk_thin_spheres/delphi.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
 
6) Now lets run blastermaster with Existing Low Dielectric Spheres
 
     blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag
 
     blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag

Revision as of 17:10, 2 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

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.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