On Wed, Nov 23, 2011, Crystal.CHIA-YU Ku wrote:
> ....and knew a step called geometry
> optimization. This step seems to change conformation of ligands. I want to
> know how great the conformation changes during RESP charge calculation
I'll try to make things clear, but there are no general answers.
1. In the am1-bcc method, one is supposed to geometry optimize the ligand
geometry (using AM1) before estimating charges. How much things change
depends on the ligand, and you don't have to do the optimization -- that
is just what is put into the default, automatic procedure.
2. For RESP, the method of obtaining the charges (via fitting an electrostatic
potential) is independent of the method for deciding which conformation (or
combination of conformations) will be used.
So, for either am1-bcc or RESP, you could decide (if you wanted) to just use
the bound conformation of the ligand. Or you could do some minimization to
find a nearby structure.
As you note, testing to see the effect of various options is probably a good
idea.
....dac
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Received on Thu Nov 24 2011 - 07:30:02 PST
