On Sat, Apr 14, 2018, leila karami wrote:
>
> Can I use Amber for md simulation of modified nucleotides in RNA?
Yes.
Many common modified nucleotides have already been parameterized. See
%A R. Aduri
%A B.T. Psciuk
%A P. Saro
%A H. Taniga
%A H.B. Schlegel
%A J. SantaLucia, Jr.
%T AMBER force field parameters for the naturally occurring modified
nucleosides in RNA
%J J. Chem. Theory Comput.
%V 3
%P 1465-1475
%D 2007
Antechamber may be able to help if you have a novel modification. But
try to use Amber atom types, not gaff ones, since these will merge
better with non-modified nucleotides in Amber force fields.
.....dac
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Received on Sat Apr 14 2018 - 18:30:03 PDT
