AMBER Archive (2009)
Subject: Re: [AMBER] ligand parameterization
From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Nov 26 2009 - 18:13:09 CST
If you want to re-parameterize a particular torsion, you do not need to
worry EXPLICITY about the 1-4 interactions. If you set the torsion
parameters of the torsion (that you want to re-parameterize) to zero, and
calculate the MM energy, that will be enough. You will subtract the QM
energy from this MM energy, and fit it to cosine functions.
For instance, let's assume that you want to re-parameterize the following
torsion where the atoms are connected to each other as follows:
..- A - B - C - D -..
Rotation around the B-C bond will give you a torsion profile for A-B-C-D
dihedral. Let's assume that in the force field, the atom types defined for
these particular atoms are as follows:
..- a - b - c - d-..
Atoms types are important because you will zero out the torsion that you
want to fit.
Let's say that you have calculated the QM energis of this
structure/molecule for different conformations (which represents rotation
around this B-C torsion). Let's say, you did k number of QM calculations.
For each conformation, you will have seperate QM energy, and call it QM_i,
where i=1 to k.
These QM energies include both the non-bonded interactions and bonded
interactions. What you want to fit is ONLY the B-C torsion. In order to do
that, you have tovcalculate the MM energies that have zero B-C torsion
energies (or terms). So, you have to create an frcmod file which will set
this particular torsion to zero. It will look like this:
------ frcmod --------
a -b -c -d 1 0.00 0.0 1.
Note that the atom types are used in the frcmod file. Let's call this
energy that does not have the B-C torsion energy as MM_not (not standing
for no torsion). You will have k number of MM_(not,i), where i=1 to k.
The difference of QM-MM_not will be fitted to (1+cos(n*phi-gamma))
functions (see the manual). There are different approaches, but I think if
you do linear-least-square fitting, that will be fine. What this assumes
is that you are not going to fit for gamma (meaning that gamma=0 or 180,
depending on the sign of the energy barrier V_n). For fitting, you can use
Mathematica or Matlab, which can easily deal with big matrices.
The confusion is, I think, about the definition of the torsional energy.
Jason is right, the torsional energy includes all the interactions (EEL,
VDW, etc.). The cosine terms in the force field equation is just the
bonded terms due to dihedrals, namely its not the torsional energy. But
that is not what you want; you just want to re-parameterize a particular
torsion to represent the QM energy surface as well as possible.
Hope this helps. Good luck.
Jason Swails wrote:
> The 1-4 interaction term is a scaled non-bonded term. It has the same
> functional form as the regular non-bonded interactions (VDW and EEL), but
> is simply scaled down. They are unique to atoms 3 bonds separated from
> another. Thus, this term will influence your dihedral profile, so you
> to account for it when you create your dihedral parameters (i.e. you do
> want to include the 1-4 effects in your dihedral fourier expansion, since
> they will then be doubly-counted in your force field).
> Note that the torsional term does NOT represent the torsional energy. In
> the amber force field, it is nothing more than a correction to account for
> effects that are not represented by the classical 1-4 interactions. A
> example is the minimum energy angle between biphenyl (C12H10). VDW and
> terms would favor a 90 degree angle between the planes of the two benzene
> rings. However, this state is quantum mechanically unfavored because it
> breaks all delocalization between the two pi systems of the benzene rings.
> Thus, the 1-4 interactions correctly place a maximum energy at a 0 degree
> separation (i.e. completely planar), but fail to put a local maximum at 90
> degrees. This effect must be accounted for by the torsional term, but you
> don't want to add the disfavoring of the completely planar angle, since
> is already accounted for by the 1-4 terms.
> I hope this helps,
> On Thu, Nov 26, 2009 at 12:19 PM, Nahoum Anthony <
> nahoum.anthony_at_strath.ac.uk> wrote:
>> Thanks for your help Dave and Jason, but your latest reply confuses me a
>> The force field equation as given p.19 of the Amber 10 manual shows
>> for bonds, angles, dihedrals, vdW (12-6 L-J), dielectric and
>> (if explicitly desired for the latter). I'd always considered the
>> term to represent the torsional energy, so where is the 1-4 interaction
>> ? is it just part of the vdW and dielectric ?
>> Thanks again for your time,
>> From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of
>> Jason Swails [jason.swails_at_gmail.com]
>> Sent: 26 November 2009 15:47
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] ligand parameterization
>> Don't forget to zero out the torsional term in the force field. The 1-4
>> interactions will account for some of the profile, so the torsion term
>> just a correction for the 1-4 inadequacies. Then you can do the same
>> with amber as you did with Gaussian and fit the difference to the
>> terms that define the torsion.
>> Good luck!
>> On Thu, Nov 26, 2009 at 10:09 AM, case <case_at_biomaps.rutgers.edu> wrote:
>> > On Thu, Nov 26, 2009, Nahoum Anthony wrote:
>> > >
>> > > I want to parameterize a ligand for which the default torsion term
>> > > in the .frcmod file by antechamber is inadequate. I've used Gaussian
>> > > do a torsion scan and get an energy plot for the full rotation and I
>> > > want to fit that energy plot using Amber's force field equation.
>> > > read several papers where people have done this sort of things, but
>> > > can never quite get if they fit the Gaussian energy with the full
>> > > field equation, allowing only the torsional parameters to vary or if
>> > > they try to fit only the torsional part of the force field equation
>> > > the Gaussian results. What is the correct procedure, if any ?
>> > The former: you need to compare the total energy from Gaussian to the
>> > energy from the force field.
>> > ...good luck...dac
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER_at_ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> AMBER mailing list
>> AMBER mailing list
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> AMBER mailing list
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