AMBER Archive (2003)

Subject: Resp Charges for large ligand.

From: Bengt Svensson (bsven_at_msi.umn.edu)
Date: Mon Mar 17 2003 - 18:11:42 CST

I want to calculate the partial charges for a large ligand to be used with
the AMBER force field. My ligand is composed of a head group and a linker.
The head group is ~60 atoms and the linker ~45 atoms, and this is the
smallest in a set of many ligands. Other ligands are up to twice that
size. The size and flexibility of the ligand makes it unpractical to use
Gaussian 98 with HF/6-31g* to calculate the electrostatic potential for
the whole molecule.

I therefore split the ligand in two fragments, like this,

       R1 - Phenyl - NH - CO - CH3

               CH3 - NH - CO - CH2 - R2

and individually ran the Gaussian calculations. I then ran Antechamber
and got the ESP file and RESP.in file s for the two stages of the charge
fit. I now need to combine the two ESP files and create an input file for
RESP to generate the partial charges for the combined molecule.

I looked at the Amber RESP adenine example. The description for the demo
states that it deals with a fit of two molecules to get charges for a
supermolecule. Exactly what I need, I thought. But the example is not like
that at all. There are two sets of ESP field points that are identical.
Also all atoms are identical between those molecules in the example. This
example is actually very different from what I want to do.

Can someone please give me some suggestions of how I can fit the charges
for the combined fragments using RESP?

Is the splitting point and the overlap between the fragments as I chose
them appropriate? Would I need more of an overlap?

Are there other RESP tutorials or examples available anywhere that would
be helpful?

Thanks,

        Bengt Svensson

------------------------------------------------------------------------------
  Dr. Bengt Svensson
  University Of Minnesota e-mail: bsven_at_msi.umn.edu
  Dept. of Medicinal Chemistry tel: +1-612-626-4429
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