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

[jiserte at unq.edu.ar]

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:
-----------------------------------------
import
chimera                                    
#1
from chimera import runCommand                     #2
runCommand('open ligands/lig_in.mol2')             #3
runCommand('addh')                                
#4
runCommand('addcharge')                           
#5
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.
javier
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140421/20a1493d/attachment.html>