Subject: Re: CCL:Semiempirical vs. empirical force fields?

From: Gregory Nikiforovich <[email-masked]>
Date: Tue, 7 Feb 1995 08:14:00 -0600 (CST)

On Mon, 6 Feb 1995, Gert von Helden wrote:

> In some situations conformation A is lower then B by 7 kcal/mol
> using amber but B is lower that A by 5 kcal/mol using PM3.
> We would like to compare the calculations to gas phase experiments. 
> So which method is better and more reliable?

  The real point is that most uncertainties in your calculations would
 probably come from your protocol (annealing) than from the type of force
 field you use. To compare calculations with any experiment you have to
 be sure you have found all (at least, the most of) low energy conformers.
 If any of them (or any of combinations of them) could explain the
 experimental data, you win. Now, in my experience, with AMBER you can
 safely assume that any conformer of your peptide within relative energy
 ca 0.5-0.7 kcal/mol*residue belongs to the low-energy family. It probably
 would give you up to 30 different possible conformers for the nonapeptide
 backbone alone. With this level of uncertainty, why be bothered with the
 question, which force field is "better"? None of them would correspond
 to the true Boltzmann distribution of conformers.

   Good luck.

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Gregory V. Nikiforovich                                   Phone (314) 935-4677
Research Professor                                        Fax   (314) 935-4979
Center for Molecular Design                            E-mail address:
Washington University                                  [email-masked]
Lopata Hall, Box 1099
St.Louis, MO 63130

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