[Chimera-users] minimize without addh and without GUI

richardbonnet richard.bonnet at u-clermont1.fr
Mon Oct 19 08:35:15 PDT 2009

Dear users

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("select @H=")
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,

Richard Bonnet
Universite Auvergne


More information about the Chimera-users mailing list