Hi Kellon,
Sorry to run this off on a tangent, but OpenFF is also trying to
incorporate the standard definitions from components.cif into some of our
own work. It's turning out to be not-entirely-trivial -- basically, we're
struggling to distinguish when entries in that file are describing residue
_substructures_ (as they'd appear in the middle of a chain), versus just an
uncapped instance of the residue as would be found floating around in
solution.
I'd be happy to loop you in on our working sessions on this, Kellon, or you
can contact me when you start working on it and I can catch you up on what
we found.
Cheers,
Jeff
On Thu, May 13, 2021 at 8:36 PM Kellon Belfon <kellonbelfon.gmail.com>
wrote:
> I am realizing the major error in that decision. Definitely it was not the
> best approach for the users and it makes automation complicated.
>
> Thank you for the resource and I would take it upon myself to volunteer for
> that task this summer.
>
>
>
> On Thu, May 13, 2021, 9:46 PM David A Case <david.case.rutgers.edu> wrote:
>
> > On Thu, May 13, 2021, Kellon Belfon wrote:
> > >
> > >I made the decision to use SED for the atom name of the Selenium based
> on
> > >the position of the atom.
> >
> > Oooh...this is not right. The wwPDB defines atom and residue names,
> > not force field developers. You can get the components.cif file, which
> > establishes the proper atom and residue names for most everything in the
> > PDB, here:
> >
> > https://www.wwpdb.org/data/ccd
> >
> > All those working on force fields should become familiar with this
> > resource.
> >
> > Not urgent, but we should examine our library files for consistency with
> > the
> > components.cif file, and create updates as needed. For now, your
> proposed
> > workaround (having the original user edit their PDB files) will allow
> work
> > to continue.
> >
> > [I've kind of learned the hard way here, myself. I was the one who
> allowed
> > Na+, K+ and Cl- continue as atom names for ions in Amber libraries. We
> > should have bitten the bullet long ago, and gone with the standard names,
> > NA, K and CL.]
> >
> > ....dac
> >
> >
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> >
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Received on Fri May 14 2021 - 08:00:03 PDT
