Dear Amber community,
I am looking for forcefield parameters of amino-acid analogs as those
with where sidechains are capped by a hydrogen atom at Cβ. I want to use
them to study amino-acid side chain interactions with come compounds and am
looking for a reasonable mode of amino-acids that lacks backbone atoms. I
will appreciate any suggestion to obtain reasonable parameters for such
analogs.
There are some studies (such as below) where authors used gromos.
Anita de Ruiter, Bojan Zagrovic, Absolute binding-free energies between
standard
RNA/DNA nucleobases and amino-acid sidechain analogs in different
environments, Nucleic Acids Research, Volume 43, Issue 2, 30 January 2015,
Pages 708–718,
https://doi.org/10.1093/nar/gku1344
Thnks,
Mish
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Received on Fri Nov 08 2024 - 13:00:02 PST
