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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Received on Thu May 13 2021 - 21:00:02 PDT
