[Chimera-users] minimize without addh and without GUI
richard.bonnet at u-clermont1.fr
Mon Oct 19 08:35:15 PDT 2009
Would you give me the best way to minimize the hydrogens in ligands with
chimera used without GUI and without addh?
I use : chimera --nogui --nostatus ligand_1.mol2 ./script.py
here is script.py :
from chimera import runCommand
runCommand("minimize freeze unselected nsteps 1000")
runCommand("write format mol2 0 out.mol2")
However, chimera add wrong hydrogen because of the load of addh with
minimize. I have a lot of ligands to process and I can not use GUI.
thank you much for your help,
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