Protein Target Preparation

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Protein Target Preparation be-blasti is still the preferred method of downloading PDB files and splitting them into rec.pdb and xtal-lig.pdb files. Run it with

be_blasti.csh filename

The filename should be a file that contains PDB codes you want to download.

Once you get a rec.pdb (representing the protein) and xtal-lig.pdb (representing the ligand or a set of atoms in the binding site of the protein) (these names can be changed as well, see options), you can run, the new version of DOCK Blaster. Try running the help to see the extensive options:

$DOCK_BASE/src/blastermaster_1.0/  -h

A typical way of running it is to just run it as:

$DOCK_BASE/src/blastermaster_1.0/ -v

-v gives you verbose output, which can be helpful if something goes wrong. If everything is successful, you'll see this at the end of the file:

copying matching_spheres.sph into dockfiles
copying trim.electrostatics.phi into dockfiles
copying ligand.desolv.hydrogen into dockfiles
copying ligand.desolv.heavy into dockfiles
copying vdw.bmp into dockfiles
copying vdw.vdw into dockfiles
copying vdw.parms.amb.mindock into dockfiles
writing INDOCK file:  INDOCK

Otherwise something went wrong. Notice that you have an INDOCK file written for you, with many defaults set that you may want to change. Also, old INDOCK files are slightly incompatible with the new files, so you should consult the changed version written for you, or take a finer look at the page on the DOCK3.7 INDOCK file.

Adding Static Waters to the Protein Structure

Flexible Docking