David,
Thanks for your helpful response.
Best,
On Fri, 23 Mar 2007, David Mobley wrote:
> Ilyas,
>
> > I am wondering if we can combine RESP and AM1-BCC results of some parts of
> > a residue to create a modified residue. I have a big residue which has a
> > backbone part similar to CYS. What I wanna do is to use antechamber to
> > create the charges for all of the atoms except the backbone ones. I want
> > to use the original resp charges of the backbone atoms while bcc charges
> > for the rest of the atoms (in this residue). I know that charge methods
> > are just to mirror the electrostatic potentials, which means we can
> > have different charge distributions for a molecule that can create the
> > same electrostatic potential effects. If someone can direct me to some
> > papers/literature discussing this issue, I will greatly appreciate it.
>
> Nobody has studied doing what you're proposing in any extensive way, I
> don't think. It is not, however, crazy, since AM1-BCC is parameterized
> to be "like" RESP HF 6/31G* charges (see the original AM1-BCC papers
> from Chris Bayly).
>
> Basically, you're facing the same problem anyone has to face when they
> want to parameterize a new sidechain: You don't want to change the
> backbone charges since those are coupled to the dihedrals, which
> you're not changing, and you need to compute charges suitable for the
> sidechain. The conventional choice would be to do a new RESP HF 6/31G*
> calculation for the sidechains and then combine that with the existing
> backbone charges. But you could argue that AM1-BCC would work just as
> well. While no one has studied this for residues, I did look at this
> for a bunch of different small molecules including the sidechain
> analogs (http://dx.doi.org/10.1021/jp0667442), and found that AM1-BCC
> was only slightly worse than RESP HF 6/31G* charges. So maybe that's
> all you need...
>
> David
>
>
> >
> > Best,
> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > - Department of Chemisty - -
> > - University of Rochester - -
> > - Hutchison Hall, # B10 - -
> > - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> > - http://www.pas.rochester.edu/~yildirim/ -
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>
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Mar 25 2007 - 06:07:52 PDT
