Re: [AMBER] Selenomethionine force field parameters

From: David A Case <>
Date: Fri, 14 May 2021 12:01:17 -0400

On Fri, May 14, 2021, Jeffrey Wagner wrote:
>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

Hi Jeff:

I'm guessing that just seeing if the chem_comp.type contains the word
"LINKING" is not enough, then. Does it help to look at the
chem_comp.pdbx_type field, searching for "ATOMP"?

Examples of failures would be helpful, as we (along with many others) are
trying to automate MM setup procedures.


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Received on Fri May 14 2021 - 09:30:02 PDT
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