Subject: min. dist. between protons

From: [email-masked]
Date: 12 Dec 94 12:36:23 SAST-2

I am working with Macromodel, and have the problem that it generates
structures in which the approach between two non-bonded hydrogens can
be as little as 1.76 Angstroms, and the energy of such interactions
is reported to be relatively low. I have used both the Amber force
field and the MM2 force field. I don't understand how such a close
interaction can have such a low energy. Can anyone please offer me an
explanation?

Kate Sunter.

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From: Gregory Nikiforovich <[email-masked]>
Date: Mon, 12 Dec 1994 06:58:15 -0600 (CST)

> interaction can have such a low energy. Can anyone please offer me an

 Looks like your protons are connected to the same carbon (CH2 group). They
 could interact in force fields you have mentioned as so called "i - i+2"
 atoms, which have an artificial energy potential, having nothing similar
 to a real situation. This is an inherent flaw for any force field using
 flexible valence geometry. Do not pay attention to this "interproton energy"
 at all.

 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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