Dear Dr. Case,
Thank you for your information. It seems like choosing which conformation
and charging your ligand are two two different business. I think I can use
prepi and frcmod files generated by RESP procedure, and the pdb life of my
ligand for its docked conformation.
I am going to use RESP charging method for my ligand. Thank you very much
for your kindly guidance and help.
Sincerely,
Crystal
On Thu, Nov 24, 2011 at 7:12 AM, case <case.biomaps.rutgers.edu> wrote:
> 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 Fri Dec 02 2011 - 14:30:03 PST
