Multimol2db.py: Difference between revisions
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SMALL | SMALL | ||
NO_CHARGES | NO_CHARGES | ||
@<TRIPOS>ATOM | @<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 | 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/ | The file is in your dockenv/scripts or $DOCK_BASE/scripts/ | ||
Revision as of 01:00, 8 February 2012
multimol2db.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 & mol2db on it to make .db files for docking.
multimol2db.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/scripts or $DOCK_BASE/scripts/
A version is also kept is ~/Source/bks_src/multimol2db.py