Thank you very much Professor Case for your explanation and Dave Cerutti's
paper - I am grateful for you!
~Kenneth
Kenneth N. McGuinness Ph.D
Research Associate
Advanced Science Research Center CUNY
Adviser: Dr. Rein Ulijn <http://www.ulijnlab.com/>
Cell: 928-925-7693
On Wed, Apr 13, 2016 at 8:59 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Wed, Apr 13, 2016, Kenneth McGuinness wrote:
> >
> > So I would like to use gaussian to calculate atomic partial charges (new
> to
> > this completely so any help would be great!)
> >
> > The paper <http://dx.doi.org/10.1080/07391102.2015.1092475>, works on
> the
> > molecule I am interested in, suggests to use the NBO method for
> calculating
> > partial charges
> >
> > I would like to/ or maybe not reproduce their results for comparison ( I
> am
> > open to suggestions since I am interested in the molecule binding to
> > proteins rather than molecule binding to carbon nanotubes as in the
> paper)
> >
> > Looking at the Amber manual: Antechamber (RESP, CM1 ... methods are read
> > in)
>
> Partial charges for molecular mechanics generally aim to be somewhat
> "over-polarized" to try to represent electrostatic interactions in water,
> not in the gas phase. In the "amber" family of force fields, the RESP
> procedure is very commonly used (see the R.E.D. website for scripts that
> make this pretty straightforward.) But there is nothing "magic" about
> the RESP procedure (it relies on systematic errors in low-level, HF
> 6-31G* calculations)--it just leads to the same mistakes for everyone.
>
> An alternative procedure that we have worked on is described in JPCB
> 117:2328, 2013. I'm not necessarily suggesting you use this, but the
> paper describes many of the tradeoffs involved in trying to find simple
> fixed charge molecular mechanics models that are appropriate for condensed
> phase simulations.
>
> You are certainly welcome to use whatever charges you wish, or which are
> recommended in papers you trust, and you can indeed just copy such charges
> into the mol2 file that antechamber would create.
>
> ...good luck...dac
>
>
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Received on Thu Apr 14 2016 - 13:30:02 PDT
