Subject: Re: CCL:Comparison of force fields

From: Scott Struthers <[email-masked]>
Date: Thu, 15 May 1997 13:13:46 -0700

At 06:24 PM 5/15/97 +0200, Oliver Kohlbacher wrote:
>Dear Netters,
>
>I'm trying to compare the total energies of different conformations of
>large protein complexes (preferably in water).
>The only obvious possibility to get these energies seems to be the use of
>a molecular mechanics force field.

This type of question comes up a lot.

I doubt you are really interested in force field calculations here.
What is the question you are asking? Relative stabilities (i.e. free
energies) of different complex structures?

If so, you should be more interested in long range electrostatics and
hydrophobic contributions to the free energy.

Mechanics (unless you do lots of very careful free energy perturbation
stuff) will only give you reasonable structures. There will be lots of noise
in the value of the energy as a function of parameters you are probably not
interested in.

check out solvation work by Honig, Eisenberg, etc for a start.

good luck

scott

----------------------------------
    R. Scott Struthers, Ph.D.
 Co-Founder/Scientific Director
       ScienceMedia Inc.

     [email-masked]
      www.sciencemedia.com