Re: [AMBER] Inconsistent Internal energy from monomer to dimer

From: Carlos Simmerling <>
Date: Sat, 7 Apr 2012 07:06:27 -0400

Perhaps you could calculate the interaction energy between the monomers to
compare. Without knowing the biophysics of your system I can't comment, but
protein dimers often have large interfaces to give specificity, but the
resulting strong interaction is modulated by strain or desolvation to give
the desired binding affinity. There are even cases of peptides that don't
even fold until they bind.
On Apr 7, 2012 5:51 AM, "Josep Maria Campanera Alsina" <>

> Thanks Carlos. So I conclude from your statements that these
> differences between the free monomer and the strained monomer of 22
> kcal/mol just in internal energy (Bond+angles+dihed) could be normal
> for Amber. I still have my doubts. Here it is a peptide monomer of 26
> residues and therefore each residue introduce an strain energy of 0.85
> kcal/mol.
> Could any one comment or sign any work or article with significant
> differences in the internal energy term between a free monomer and a
> strained monomer? That would be extremely useful.
> All the best,
> Josep M.,
> Message: 24
> Date: Thu, 5 Apr 2012 10:49:43 -0400
> From: Carlos Simmerling <>
> Subject: Re: [AMBER] Inconsistent Internal energy from monomer to
> dimer
> To: AMBER Mailing List <>
> Message-ID:
> <>
> Content-Type: text/plain; charset=ISO-8859-1
> as was said before, it's entirely reasonable that the interactions between
> the monomers is strong enough to cause some internal strain in the
> individual monomers as compared to their free structures. in fact, it's
> probably unlikely that the monomers have the identical structure when bound
> as when unbound.
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Received on Sat Apr 07 2012 - 04:30:03 PDT
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