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 reparameterize a particular torsion, you do not need to
worry EXPLICITY about the 14 interactions. If you set the torsion
parameters of the torsion (that you want to reparameterize) 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 reparameterize the following
torsion where the atoms are connected to each other as follows:
.. A  B  C  D ..
Rotation around the BC bond will give you a torsion profile for ABCD
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 BC 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 nonbonded interactions and bonded
interactions. What you want to fit is ONLY the BC torsion. In order to do
that, you have tovcalculate the MM energies that have zero BC 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 
.
.
.
.
DIHE
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 BC 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 QMMM_not will be fitted to (1+cos(n*phigamma))
functions (see the manual). There are different approaches, but I think if
you do linearleastsquare 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 reparameterize a particular
torsion to represent the QM energy surface as well as possible.
Hope this helps. Good luck.
Jason Swails wrote:
> Hello,
>
> The 14 interaction term is a scaled nonbonded term. It has the same
> functional form as the regular nonbonded interactions (VDW and EEL), but
> it
> is simply scaled down. They are unique to atoms 3 bonds separated from
> one
> another. Thus, this term will influence your dihedral profile, so you
> need
> to account for it when you create your dihedral parameters (i.e. you do
> not
> want to include the 14 effects in your dihedral fourier expansion, since
> they will then be doublycounted 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 14 interactions. A
> good
> example is the minimum energy angle between biphenyl (C12H10). VDW and
> EEL
> 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 14 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
> that
> is already accounted for by the 14 terms.
>
> I hope this helps,
> Jason
>
> 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
>> bit...
>> The force field equation as given p.19 of the Amber 10 manual shows
>> terms
>> for bonds, angles, dihedrals, vdW (126 LJ), dielectric and
>> polarization
>> (if explicitly desired for the latter). I'd always considered the
>> dihedral
>> term to represent the torsional energy, so where is the 14 interaction
>> term
>> ? is it just part of the vdW and dielectric ?
>>
>> Thanks again for your time,
>>
>> Nahoum
>>
>> ________________________________________
>> From: amberbounces_at_ambermd.org [amberbounces_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 14
>> interactions will account for some of the profile, so the torsion term
>> is
>> just a correction for the 14 inadequacies. Then you can do the same
>> scan
>> with amber as you did with Gaussian and fit the difference to the
>> fourier
>> terms that define the torsion.
>>
>> Good luck!
>> Jason
>>
>> 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
>> given
>> > > in the .frcmod file by antechamber is inadequate. I've used Gaussian
>> to
>> > > 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.
>> I've
>> > > read several papers where people have done this sort of things, but
>> I
>> > > can never quite get if they fit the Gaussian energy with the full
>> force
>> > > field equation, allowing only the torsional parameters to vary or if
>> > > they try to fit only the torsional part of the force field equation
>> to
>> > > the Gaussian results. What is the correct procedure, if any ?
>> >
>> > The former: you need to compare the total energy from Gaussian to the
>> total
>> > 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
>> 3523924032
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>>
>
>
>
> 
> 
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 3523924032
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
Ilyas Yildirim

 Department of Chemisty  
 University of Rochester  
 Hutchison Hall, Office B10  
 Rochester, NY 146270216  
 Ph.:(585) 275 67 66 (Office)  
 Homepage: 
 http://www.pas.rochester.edu/~yildirim/ 

"Carpe Diem !"
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