[Chimera-users] Problem with charges when writing mol2 file with a python script.

jiserte at unq.edu.ar jiserte at unq.edu.ar
Mon Apr 21 09:59:20 PDT 2014

I'm trying to write a simple python script to open a mol2 file with a
ligand, add hydrogens, add charges and write it into another mol2.
The script is this:
from chimera import runCommand                     #2
runCommand('open ligands/lig_in.mol2')             #3
runCommand('write format mol2 #0 lig_out.mol2')    #6
The result mol2 file does no contain any charges.
However, if a run another script that is exactly like this but does not
contain the last line (#6),  and then
execute the command 'write format mol2 #0 lig_out.mol2' manually, the mol2
file contains charges.
I don't understand why there is a difference with both methods.
best regards.
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