# 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 $mud/topdock.py -e. If one wants to create an .eel1 file for a different subset of the molecules, first create the list of molecule names plus their energies (on one line) and then feed it to getxpdb.pl name_energy.list < FF.test.eel1 > subset_name.eel1. ## Getting individual atom contributions with scoreopt_so ### First you need and .eel1 file to be scored # For the xtal-lig.mol2 in its crystallographic pose Convert an input .mol2 file into an .eel1 file • run amsol as described here to calculate atomic solvation energies. • run 'file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1'. # For molecules that have already been docked • run '$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 .
• 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 .
• the van der Waals interaction energy is calculated as ${vdW}_{(r)}=\frac{A}{r^{12}}-\frac{B}{r^6}=a-b$. In every ATOM line, columns 9, 10 and 11 are $a$, $b$ and $a-b$, 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.