[MMTK] Triple bonds?

Ramon Crehuet rcrehuet at gmail.com
Thu Jul 7 08:27:58 UTC 2011

Dear Christopher,
Considering the amount of human time vs. computer time, and if the molecules
are smallish as you said, why don't you go for a QM method? Semi-empirical
methods can treat prettly large molecules and you will not need to
parameterize anything.
Of course, this can't be done with MMTK. Before choorsing another software,
make sure it has analytical second derivatives of the energy. Otherwise,
frequencies are rather slow to calculate. If you do need to work with MMTK
afterwards, you can always write a parser that reads the QM outputs and
generates ScientificPython vectors. I think this is still less work than a
thorough parameterization.

2011/7/7 Konrad Hinsen <research at khinsen.fastmail.net>

> 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.
> --
> ------------------------------**------------------------------**---------
> 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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