[MMTK] Triple bonds?

Konrad Hinsen research at khinsen.fastmail.net
Thu Jul 7 08:01:53 UTC 2011


On 6 Jul 2011, at 15:13, Christopher Drost wrote:

> (1) The first question I have regards sp-hybridization. My molecule
> has both C-C and C-N triple bonds, which can be something like 50-100%
> stiffer than double bonds, and prefer a different bending geometry. So
> I have to specify the sp-hybridization somehow. I've found
> documentation for specifying these in Allinger's MM models, but I'm
> still uncertain how to specify a triple bond for the Amber99 force
> field as implemented in MMTK. Can anyone help with how this might be
> specified? I have trouble believing that Amber99 would be ~15 years
> behind the MM models.

Amber doesn't have the notion of a double or triple bond. The molecule  
topology specifies just a bond, without any parameters. The  
interactions are then specified in terms of atom types. To get a  
triple bond, you thus have to introduce new atom types for the atoms  
on either side of the bond, and then define an appropriate force  
constant for a bond between the atoms of the corresponding types. This  
would typically be done in the form of a "modification file" (in Amber  
terminology), i.e. an extension to the list of standard Amber  
parameters. MMTK uses standard Amber modification files, so you can  
follow the Amber documentation for the details:

	http://ambermd.org/#ff

> with an initial "configuration". You might want to fix this to be a
> more verbose error message.

Indeed. There isn't much I can do about the fundamental problem that  
energy minimization requires an initial configuration, but I can add a  
check for this condition.

> (3) One limitation: my molecules have a net dipole moment. (Probably
> the benzene C-H bonds do as well?) I don't yet know how to calculate
> the proper 'amber_charge' values in such a case.

There are no special precautions. If you know the dipole moment of  
benzene, you could use it as a constraint in the charge fitting  
procedure. Otherwise you just fit the charges and accept whatever  
dipole moment they result in.

> There is some documentation about the ChargeFit class but I can't  
> really divine how
> it works, exactly. So, does anyone have an example for calculating
> these amber_charge parameters, something like the way that Amber's
> energy minimization algorithm can be used to calculate their
> positions?

Charge fitting first of all requires values for the electrostatic  
potential around the molecule, which you would typically get from  
quantum chemistry calculations. Do you have those? If yes, have a look  
at Examples/Miscellaneous/charge_fit.py for a simple example of how to  
use the charge fit module.

Of course it might be worth checking first if someone else has already  
computed Amber parameters for benzene. Or for the OPLS force field,  
which is also supported by MMTK and often a better choice for working  
with non-biological molecules. OPLS uses the same functional form as  
Amber, but has different atom types and different parameters.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net
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