This Module facilitates selecting and formatting a ligand for a subsequent AutoDock run. The steps in this process are:

• The user selects the small molecule from a list of molecules already in the moleculeViewer OR as a PDBQ file or as a MOL2 file from a fileBrowser.

  • The user selects the ROOT atom of the ligand either:

    • by picking it or

    • by autoroot which sets the root to be the atom in the molecule which has the smallest largest sub-tree.

• Next the user decides which possible and active torsions he wants to disallow, changing them from active to inactive. This is done by picking an active green bond which turns it inactive or purple. This is reversible. The user can also disallow all peptide backbone torsions and/or all torsions of amide bonds.

• Carbons in cycles can be tested for aromaticity. If the angle between the normals to adjacent atoms in the cycle is less than 7.5 Degrees, the cycle is considered aromatic: its carbons are renamed "A.." and their element type set to A. (This is for the force-field calculations done in AutoDock.) This Module does this conversion reversibly. Also, the user is able to select a carbon to convert (reversibly).

• Non-polar hydrogens can be merged which means that the charge of each is added to its carbon and the hydrogen atoms themselves are not written in the output file, thus in some sense removing them from the molecule. Fewer atoms simplifies the AutoDock run.

• The last function of this Module is to write a file which contains the correctly formatted ligand atoms. The ROOT section of the molecule expands from the selected ROOT atom out to include all atoms adjacent to it up to the first active torsion. The active torsions set the position of BRANCH and TORS key words in the output pdbq file (and their corresponding ENDBRANCH and ENDTORS key words). These keywords are nested to set up a Depth-First Order Traversal. Autotors also calculates the torsional degrees of freedom (TORSDOF) which is the number of possible torsions less the number of symmetry-equivalent torsions (such as a bond to a NH3). This key word is the last line of the pdbq file.

checkMolCharges ( mol,  vf )

initModule ( vf )