Analysing the results

Some analyses that can be performed

Combining the results of all subdirectories

• in the subdirectory that contains all the individual directories for each chunk of the library, run $mud/combine.py. Then generate a file containing the top 500 molecules using '$mud/topdock.py -o top500.pdb', which you can read into ViewDOCK in chimera as a DOCK 4, 5, or 6 style file.
• to create an .eel1 file containing the top 500 molecules just run $mud/topdock.py -e. If one wants to create an .eel1 file for a different subset of the molecules, first create the list of molecule names plus their energies (on one line) and then feed it to getxpdb.pl name_energy.list < FF.test.eel1 > subset_name.eel1.

For the xtal-lig.mol2 in its crystallographic pose

Convert an input .mol2 file into an .eel1 file

• run amsol as described here to calculate atomic solvation energies.
• run 'file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1'.

For molecules that have already been docked

• run '$mud/topdock.py -e -o top500.eel1' to generate an .eel1 containing the top 500 docked molecules.
• or unzip the dock output 'gunzip -c test.eel1.gz > test.eel1'
• or to create an .eel1 file for a different subset of the molecules, first create the list of molecule names plus their energies (on one line) and then feed it to 'getxpdb.pl name_energy.list < FF.test.eel1 > subset_name.eel1'.

Individual contributions to the coulombic energy

• start scoreopt_so and choose option '2' in the first menu.
• enter the name of the DelPhi potential file, presumably grids/rec+sph.phi.
• enter the name of the ligand file, i.e., ligand.eel1 or top500.eel1.
• enter the name of the output file, e.g. ligand.elec .
• in every ATOM line, columns 9, 10 and 11 are the partial charge, the electrostatic field and the energy in kT (i.e., 9 × 10) of the atom, respectively.
• the DelPhi electrostatic score is the sum over the entries in column 11 times 0.5924 (conversion from kT to kcal/mol) and can be compared to the elect column in OUTDOCK.

Individual contributions to the van der Waals energy

• start scoreopt_so and choose option '3' in the first menu.
• enter the prefix name of grids for ff scoring as a full path, i.e., grids/chem .
• enter the name of the van der Waals parameter file, presumably grids/vdw.parms.amb.mindock .
• answer the question about interpolation with 'yes'.
• enter a sufficiently large number as maximal van der Waals energy, e.g. 10000.
• enter the name of the ligand file, i.e., ligand.eel1 .
• enter the name of the output file, e.g. ligand.vdw .
• be adequately scared.
• the van der Waals interaction energy is calculated as <math>{vdW}_{(r)}=\frac{A}{r^{12}}-\frac{B}{r^6}=a-b</math>. In every ATOM line, columns 9, 10 and 11 are <math>a</math>, <math>b</math> and <math>a-b</math>, respectively.
• DO NOT use the interaction energy, as we only use the vdw component now. Instead, use the vdwsum to compare with the vdW column in OUTDOCK.

Individual contributions to the desolvation

• start scoreopt_so and choose option '4' in the first menu.
• enter the name of the grid for partial desolvation, presumably grids/solvmap .
• enter the name of the ligand file, i.e., ligand.eel1 .
• enter the name of the output file, e.g. ligand.solv .
• in every ATOM line, columns 9, 10, and 11 are the total atomic solvation energy (polar + apolar), percentage desolvation, and atomic desolvation energy (i.e. - 9 × 10) of the atom, respectively.
• the total desolvation is the sum over the entries in column 11 and can be compared to the sum of the polsol and apolsol columns in OUTDOCK.

Other small useful things

Obtaining the net charge of a docked molecule

• take the output .eel1 file and run molcharge_pdb.pl < output.eel1. This will output the sequential number of the molecule, the ZINC identifier, the total charge and the number of atoms for every molecule in the file.