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

From: Josep Maria Campanera Alsina <>
Date: Wed, 4 Apr 2012 09:40:56 +0200

I undertook also the test that Carlos suggests but the result was
consistent with dimer energies. I splitted up the dimer into two
monomer trajectories and later on I computed the MMGBSA for each of
them. The result was an internal energy (BOND, ANGLES, DIHED) of
approximately for each trajectory of 567 kcal/mol (1135.89/2) whereas
the INT energy for the free monomer was computed 545 kcal/mol so a
difference of 22 kcal/mol.

In line of what Carlos says is the fact that the BOND term is
consistent between monomer and dimer (it doubles its value) but the
origin of the inconsistency are the ANGLES and DIHED terms. See the
attached file. However how can it be a 22 kcal/mol difference in the
internal energy between a free monomer and monomer with the
constraints of a partner? I think something is wrong here.

All comments will be welcome. Thanks Carlos.

Josep Maria,

> Message: 1
> Date: Tue, 3 Apr 2012 07:25:32 -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
> in order to check the code, I think the right way to go is to use ptraj to
> split the dimer trajectory into 2 monomer trajectories. then the
> conformations are the same, so the energies should match. I can completely
> expect that the dimer trajectory has different structure than the monomer,
> and so the dihedral energies are different. perhaps the dimer optimizes
> nonbonded interactions, and in the monomer the dihedrals can relax wityhout
> the nonbonded constraints.
> On Tue, Apr 3, 2012 at 7:15 AM, Josep Maria Campanera Alsina <
>> wrote:
>> Dear all,
>> I have found an inconsistency in MMGBSA/PBSA calculations that
>> embittering me. This is about the internal INT term (BOND+ ANGLES
>> +DIHEDRALS) in the MMGSBA decomposition only. A colleague has passed
>> to me two simulations run apparently under the same conditions in
>> AMBER11. One simulation consists of a peptide of 26 residues (408
>> atoms) and the other one a dimer of the SAME peptide with 52 residues
>> (816 atoms), the double of the same atoms. I've run the MMGBSA
>> analysis (AMBER11 perl and python scripts) and the INT term
>> (BOND+ANGLE+DIHED) of the DIMER (1135.89 kcal/mol) is not, by far, the
>> double of the INT term of the MONOMER (545.67 kcal/mol). I would just
>> expect approximately a double value. Actually, there is a difference
>> of 22 kcal/mol (1135.89/2-545.67)!!!!!!!!
>> Here is my question, How can be that the internal energy per monomer
>> unit changes so much? I think it cannot be! BOND, ANGLES AND DIHED
>> cannot be so different in both systems, actually should be very
>> similar in terms of monomer units. I've been trying a lot of things
>> (topology files, amber inputs etc.) to correct this but I haven't
>> found anything strange, neither in the dynamics nor in the MMGBSA!
>> What do you think? Is this energy values normal? What's wrong here?
>> Where should I focus?
>> All comments will be welcome.
>> Josep M.,
>> PD: Find attached amber files for inspection.
>> _______________________________________________
>> AMBER mailing list

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Received on Wed Apr 04 2012 - 01:00:03 PDT
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