AMBER Archive (2003)

Subject: Re: Resp Charges for large ligand.

From: John Bushnell (bushnell_at_chem.ucsb.edu)
Date: Mon Mar 17 2003 - 18:47:33 CST

  I had to work up some charges for a polymer, and ended up splitting
things up into custom residues. The key is to make the total charge
on each residue exactly equal to 0.0 or 1.0 or whatever integral
charge. So you have to use some common sense as to where you
want to split your large molecule, and what sort of end groups to
add for the ab-initio calculation, etc. I ended up hand-editing
the charges in a couple places to make them add up right, but after
the new residues were set up, I just pasted them together using
the 'sequence' command in xleap.
  I think the tutorial you mention is using multiple conformations
of the same molecule in order to get a compromise between them for
dynamic studies.

  Hope that helps - John

On Mon, 17 Mar 2003, Bengt Svensson wrote:

> 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
> 8-101 Weaver-Densford Hall fax: +1-612-626-4429
> 308 Harvard St. SE
> Minneapolis, MN 55455
> USA Visiting addr: 7-125D Weaver-Densford Hall
>