AMBER Archive (2000)

Subject: Re: CCL:froce field parameters

From: xin_hu (xxh0541_at_hotmail.com)
Date: Fri Dec 22 2000 - 12:05:09 CST

Hi, Christian: Would you please give the details about the MMFF94. I like your
idea. How do you think about the Zn ?

xin

Christian Pilger wrote:

> Dear colleagues,
>
> in my current project I have been working with AMBER 6.0. I try to
> calculate the energies of binding of different orientations of a small
> moelcule within a protein. Though AMBER contains a lot of parameters for
> non-protein atoms, the variety of my small molecule is not entirely
> covered. As I don't have enough experience to parameterize the missing
> bonds, angles, and dihedrals on my own, I was thinking of taking these
> >from the MMFF94.
>
> I could imagine two ways:
>
> 1. to borrow only those parameters for the small molecule, that are
> missing within AMBER, applying some scaling to the force constants
>
> 2. to use the MMFF94-parameters for the entire small molecule without any
> scaling, while treating the protein with the AMBER parameters
>
> Concerning the electrostatics I intend to stay with the AMBER philosophy,
> employing the RESP methodology.
>
> At the initial stage, I'm just interested in calcualting relative
> energies, i.e. rank different conformations/orientations of the same
> inhibitor with a given protein conformation.
>
> Do you think, such a strategy would be reasonable ?
>
> Any comments are welcome.
>
> Merry X-mas & guten Rutsch,
>
> Christian
>
> -----------------------------------------------------------------
>
> Dr. Christian Pilger
>
> Istituto di Strutturistica Chimica "Giordano Giacomello"
> C.N.R. - Sezione di Trieste
> Area Science Park - Basovizza
> Strada Statale 14 - Km. 163.5
> I-34012 Trieste/Italy
>
> Tel.: +39+040+226881
> Fax : +39+040+9221126
> e-mail: cpilger_at_oc30.uni-paderborn.de
>
> -----------------------------------------------------------------
>
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--
*************************************************
   Xin Hu
   Department of Pharmaceutical Science
   College of Pharmacy
   North Dakota State University
   Fargo, ND 58105
   Tel: 701-231-8298 (O)
         701-231-4360 (H)
   Fax: 701-231-7781
   E-mail: Xin_Hu_at_ndsu.nodak.edu
              xxh0541_at_hotmail.com
*************************************************