AMBER Archive (2008)

Subject: Re: AMBER: Electrostatic Energy Components

From: Carlos Simmerling (
Date: Sat Nov 22 2008 - 11:41:48 CST

the procedure should be to
1) calculate the QM energy profile for rotating the bond
2) zero the MM dihedral (cosine) terms for the rotation in question,
leaving all other parameters present, such as nonbonds
3) calculate the MM energy profile using this model
4) calculate the DIFFERENCE between the QM and MM profiles
5) fit the cosine terms to the difference (never to the actual QM profile!!)

On Fri, Nov 21, 2008 at 7:12 PM, Ilyas Yildirim
<> wrote:
> Dear Ross,
>> Note, however that I have seen many times where people try to fit their own
>> parameters and they produce a nice QM dihedral profile and then just fit the
>> dihedral term to this (forgetting all about including the 1-4 EEL and VDW
>> terms as well). Hence what they actually think they have fitted to they have
>> not and when they then include it in a large simulation they don't realize
>> that their actual force field parameters are bogus since they forgot the 1-4
>> contributions.
> Thanks for your explanations, but I could not understand this paragraph
> of yours. Let's say we have created a nice QM profile of a particular
> torsion. To do the fitting, the MM energy without the dihedral energy of
> this particular torsion should be calculated (let's call it MM_1). This
> means that an frcmod file with zero torsional barrier of the particular
> torsion needs to be used. Then, QM-MM_1 is calculated, which is fitted to
> the desired cosine terms. If the fitting will include 2 cosine terms, for
> example, QM-MM_1 should be fitted to V_1 * (1+cos(n1*x)) + V_2 *
> (1+cos(n2*x)).
> In the whole above process, the 1-4EEL and VDW terms are not
> used/calculated explicitly. They are included in the MM_1
> energy implicitly. Did you mean that? Thanks.
> Best regards,
> --
> Ilyas Yildirim, Ph.D.
> ---------------------------------------------------------------
> = Hutchison Hall B#10 - Department of Chemistry =
> = - University of Rochester =
> = 585-275-6766 (office) - =
> = =
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