Using thin spheres in DOCK3.7: Difference between revisions
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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 >& | /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 23:42, 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