Multimol2db2.py

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multimol2db2.py

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.

multimol2db2.py input.mol2

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

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/src/mol2db2/ or $DOCK_BASE/src/mol2db2

A version is also kept is ~/Source/rgc_src/multimol2db2.py

User:Rgc