Absolutely - it would become a misnomer at best. How about something called
different than MMFF94, like JDFF (completely contrived name, for arguments
sake ;)) that's using MMFF94/UFF under the hood and adds the amide
constraint under the hood?
On 16 May 2014 19:41, Greg Landrum <greg.land...@gmail.com> wrote:
>
> On Fri, May 16, 2014 at 2:22 PM, Jan Domanski <jan...@gmail.com> wrote:
>
>> Yup, David you're correct I think the code is in but Paolo guessed the
>> intentions of my question.
>>
>> I appreciate the point about amides (and other planar groups) in
>> unconstrained minimization, that's totally fair. Let me put it on its head:
>> what I would like is the constrained minimization being the default
>> behavior. Take my molecule, identify amides or other special/planar groups,
>> add constraints and minimize. Forget the unconstrained minimization - I'm
>> lazy and want my amides planar without all the code Paolo and I exchanged
>> in this thread (conformers.py scrip) ;)
>>
>> Is this totally outrageous? I'm happy to contribute bits from the
>> conformers.py Paolo and I concocted.
>>
>
> Paolo was very careful to implement MMFF94 as it was originally defined
> and published. I believe that this is a good thing.
> Any changes that affect the default behavior of the force field would mean
> that it's no longer the same thing at all. MMFF94-like is a different beast
> entirely.
>
> I believe that what you're asking for would mean doing exactly this.
>
>
> -greg
>
>
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