From chemistry-request@ccl.net Thu Jun 20 09:25:50 1991
Date: Thu, 20 Jun 91 08:28:01 -0400
From: zheng@retina.chem.psu.edu (Ya-Jun Zheng)
Subject:  More on: Free-energy perturbation calcs of zinc<->peptide binding
Status: RO

==================

>Hello to all AMBER gurus out there:
>
>I want to do a slow-growth free-energy perturbation calculation to estimate
>the Gibbs free-energy change for the process zinc-ion + peptide -> peptide.
>
>I have parameterised the zinc-ion in AMBER 3.0A as an 'H-bonding' type 
>of atom ie. it has 10-12 well-depth and equilibrium bond distances with
>all relevent donor atoms on the peptide (peptide C=O, carboxylate-O,
>amine H2N's etc).  In addition, it has a point-charge calculated by fitting
>the electrostatic potential with MOPAC.  Thus the Zn<->donor atom interaction
>energy has two major sources (i) electrostatics and (ii) 10-12 well-depth.
>
(...)
>
>Any comments about the treatment of the zinc-ion <-> peptide binding ?
>
>Looking forward (I think) to some discussion ....
>
>----
>Alan Arnold             	     |  Phone: +61 62 68 8080
>Chem. Department,University College  | ACSNET: apa@ccadfa.oz 
>Australian Defence Force Academy     |   UUCP: ...!seismo!munnari!ccadfa.oz!lpb 
>CANBERRA  ACT 2600 Australia         |   ARPA: apa%ccadfa.oz@SEISMO.CSS.GOV

  I want to add one thing. Kenneth Merz developed a AMBER force field for Zn
laterly. It works well for the compounds investigated. His approach is similar
to Alan Arnold's. It would be very interesting to compare these two. By the way
Could you post your parameters here?


Ya-Jun Zheng
Penn State University