AMBER Archive (2007)

Subject: Re: AMBER: Combining RESP with AM1-BCC

From: David Mobley (dmobley_at_gmail.com)
Date: Fri Mar 23 2007 - 17:17:50 CST

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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