Subject: froce field parameters

From: Christian Pilger <[email-masked]>
Date: Fri, 22 Dec 2000 18:31:16 +0100

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

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 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: [email-masked]
 
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From: xin_hu <[email-masked]>
Date: Fri, 22 Dec 2000 12:05:09 -0600

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:

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