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 <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] Inconsistent Internal energy from monomer to
dimer
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAGk3s-TKMUHwzQJjSLZhUv8oFb+d8MHFv8w+Avq9rJ3T3j6OMA.mail.gmail.com>
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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 - 03:00:03 PDT
