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

[Chris S. <ctsa@u.washington.edu>]

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
> >>>
> >>>
> >>>
> >>>-------------------------------------------------------
> >>>This sf.net email is sponsored by:ThinkGeek
> >>>Welcome to geek heaven.
> >>>http://thinkgeek.com/sf
> >>>_______________________________________________
> >>>Btk-developers mailing list
> >>>Btk...@li...
> >>>https://lists.sourceforge.net/lists/listinfo/btk-developers
> >>>
> >>
> >>
> >>
> >>-------------------------------------------------------
> >>This sf.net email is sponsored by:ThinkGeek
> >>Welcome to geek heaven.
> >>http://thinkgeek.com/sf
> >>_______________________________________________
> >>Btk-developers mailing list
> >>Btk...@li...
> >>https://lists.sourceforge.net/lists/listinfo/btk-developers
> >>
> >
> >
> >
> >
> > -------------------------------------------------------
> > This sf.net email is sponsored by:ThinkGeek
> > Welcome to geek heaven.
> > http://thinkgeek.com/sf
> > _______________________________________________
> > Btk-developers mailing list
> > Btk...@li...
> > https://lists.sourceforge.net/lists/listinfo/btk-developers
>
>
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Btk-developers mailing list
> Btk...@li...
> https://lists.sourceforge.net/lists/listinfo/btk-developers
>