Re: [AMBER] Selenomethionine force field parameters

From: David A Case <>
Date: Thu, 13 May 2021 21:45:09 -0400

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.]


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Received on Thu May 13 2021 - 19:00:02 PDT
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