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

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(Created page with "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_sph...")
 
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4) run thin sphere code:
 
4) run thin sphere code:
  /mnt/nfs/home/tbalius/zzz.svn/dockenv/trunk/etc/thin_spheres.py -i rec.ms -o delphi.sph >& sph/thin_spheres.log
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  /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.  
 
Note that this is avalible through the DOCK3.6 release.  

Revision as of 16:42, 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

6) Now lets run blastermaster with Existing Low Dielectric Spheres

   blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag