This script is a utility program that takes as input a .mol2 file that has been protonated and all conformations have been generated with OMEGA (or alternatively, a mol2 file from some other source) and runs AMSOL & mol2db2 on it to make .db2 files for docking.
It is very important that the beginning of your .mol2 file contains this kind of header:
@<TRIPOS>MOLECULE TEMP12345678 70 72 0 0 0 SMALL NO_CHARGES @<TRIPOS>ATOM 1 C1 5.1180 4.5740 2.9690 C.3 1 UNK1 0.0182 2 N1 4.4470 5.0610 4.2130 N.4 1 UNK1 -0.5553
Otherwise AMSOL and the associated scripts that run it will crash. The most important part is the second line that needs to be in the form XXXX00000000
1. Don't have any extra lines except the MOLECULE, ATOM and BOND records
2. The last 3 columns of the atom record are important (the 1 UNK1 0.0182), some .mol2 files don't have them so just add dummy (1 UNK1 0.0000) to yours.
The file is in your dockenv/src/mol2db2/ or $DOCK_BASE/src/mol2db2
A version is also kept is ~/Source/rgc_src/multimol2db2.py