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

From: Carlos Simmerling <>
Date: Thu, 5 Apr 2012 10:49:43 -0400

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.

On Thu, Apr 5, 2012 at 7:11 AM, Josep Maria Campanera Alsina <> wrote:

> Sorry,
> I rewrite my previous email clearer.
> .The internal energy (BOND+ANGLES+DIHED) for the dimer (AB) was
> computed 1136 kcal/mol.
> -The internal energy of the splitted monomers (A and B that come from
> the AB dimer) was slightly different between both monomers but around
> the value of 567-568 kcal/mol. Lets say 569 kcal/mol for one and 567
> kcal/mol for the other one. I do not have the exact values with me now
> but they weren't much different. These values are consistent with the
> AB value.
> -The internal energy for the free monomer was computed to be 545
> kcal/mol. This value doesn't match with the dimer AB value of Internal
> energy.
> All comments are welcome. I've attached the output files for
> inspection in previous emails.
> All the best,
> Josep M.,
> Message: 16
> Date: Wed, 4 Apr 2012 05:37:37 -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
> i'm not sure i understand your statements here, and I want to make sure its
> clear.
> you calculated 3 trajectory energies- the dimer trajectory (AB), and then
> each of the 2 monomers from the same trajectory (A+B). You're saying that
> A+B still isn't equal to AB. I'm asking because below you only quote 2
> energies, and I'm not sure if you mean to say that the split monomers had
> identical energies (possible, but seems unlikely).
> If this is the case, then something is clearly wrong with the energy
> calculations (or perhaps in the inputs).
> Can you confirm, and provide all 3 energy values?
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Received on Thu Apr 05 2012 - 08:00:05 PDT
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