Difference between revisions of "Multimol2db.py"

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(explaining how henry broke everything)
m (added some tips to get this to work from Nir)
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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

User:Rgc