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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 & mol2db on it to make .db files for docking. input.mol2

It is very important that the beginning of your .mol2 file contains this kind of header:

   70    72     0     0     0

    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

Other tips:

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/scripts or $DOCK_BASE/scripts/

A version is also kept is ~/Source/bks_src/


Crucial tip:

You have to add the correct header to the db.db.gz file:

DOCK 5.2 ligand_atoms
positive                       (1)
negative                       (2)
acceptor                       (3)
donor                          (4)
ester_o                        (5)
amide_o                        (6)
neutral                        (7)