Re: [Btk-developers] generic molecule self-energy

[Tim R. <timr@u.washington.edu>]

Maybe I spoke too soon.  I think your first suggestion is the correct 
way to do self energies (function taking BuildableMolecule class).  The 
upshot, of course, is that we actually need a BuildableMolecule class, 
which wasn't clear before.

so,

double SelfEnergy(BuildableMolecule const & mol);

(it *could* be a template, of course, if the need arose.  We'd just need 
  a way to query the molecule for it's connectivities.  This might come 
up later with complexes.  Bridge.cross(when_we_come_to_it) )

-tim

Chris Saunders wrote:
> for ques 1)
> I don't know what the latest decision is on what actually gets passed to
> the energy function to calc the self-energy of a molecule. If it were the
> molecule itself, then undefined would mean that the self energy function
> would take a "Buildable Molecule" class. If it's going to be some kind of
> atom iterator, than craming the topology information into some
> data-structure visible to the energy function is going to have to be
> worked out before we really care about how to deal with the 'Generic
> Molecule' exception. In general , by undefined, I mean that it shouldn't
> even compile if you throw the wrong class at a self-energy function.
> 
> 
> 
> On Wed, 24 Jul 2002, Tim Robertson wrote:
> 
> 
>>This might be tricky to implement.  Unless, by "undefined" you mean
>>"energy function will spit out a value, but value will be meaningless."
>>  Then it's not so hard.
>>
>>Regarding topology files -- the plan is not to include anything charmm
>>or amber specific in the molecule class itself, right?   I'm thinking
>>that you need functions like Molecule::define_connectivity() (or some
>>such thing), that an outside method would call to set up the tetrads.
>>
>>Is this the plan (or something like it) ?
>>
>>-tim
>>
>>Chris Saunders wrote:
>>
>>>well what I mean is that atoms seperated by 1,2, or 3 covalent bonds will
>>>have their vdw and electostatic interactions scaled down. This means that
>>>the topology would have to be known or calculated for any molecule before
>>>a self-energy could be found. Any molecule that has a topology file
>>>available, as you suggest, is no longer generic -- so it sounds like what
>>>we'll have to say is that for true generic molecules (3d positions and
>>>atom types ONLY )  the self-energy is undefined.
>>>
>>>-c
>>>
>>>On Wed, 24 Jul 2002 EJ...@lb... wrote:
>>>
>>>
>>>
>>>>I'm not sure exactly what you mean by bonded scale-downs, but my plan was to
>>>>use the topology/param files the same way the MD packages do.  The files give
>>>>a list of specific atom names and and connectivities and parameters that
>>>>correspond to them.  So to parameterize a generic molecule, you'd just pass the
>>>>molecule and a param file to some function that would then assign the tetrads
>>>>and radii and charge ...
>>>>
>>>>Does that answer the question?
>>>>
>>>>-E
>>>>
>>>>----- Original Message -----
>>>>From: Chris Saunders <ctsa@u.washington.edu>
>>>>Date: Wednesday, July 24, 2002 2:27 pm
>>>>Subject: [Btk-developers] generic molecule self-energy
>>>>
>>>>
>>>>
>>>>>Folks,
>>>>>Is there a plan to deal with bonded scale-downs for generic
>>>>>moleculesenergy calculations? For moledules with defined
>>>>>topologies, we can either
>>>>>use generic 1-2,1-3, and 1-4 bond energy scaling rules, or write
>>>>>proteinand dna specific rules (as in the off-the-cuff ruleset in
>>>>>rosetta). When
>>>>>dealing with generic molecules, is the solution to just define bonds
>>>>>automatically based on atom-pair distances, OR is there really no
>>>>>need to
>>>>>find the self-energy of a generic molecule?
>>>>>
>>>>>-c
>>>>>
>>>>>
>>>>>
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