Re: [AMBER] Selenomethionine force field parameters

From: Kellon Belfon <>
Date: Thu, 13 May 2021 23:35:25 -0400

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 <> 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:
> 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
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