Dear Alessandro,
Notice, you can get the new version of AMBER Tools (19) free for academics from the website.
You can check the following paper for an update on DNA force fields:
# How accurate are accurate force-fields for B-DNA? NAR, 2017 [
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397185]
From which I would say parmbsc1 or OL15 are very good choices (both already implemented in AMBER since AMBER Tools 16). I prefer the former parameter set but it's a matter of taste... however, both force fields should run OK on older version of the code...
I'm not familiar in using polarizable force fields, but there seems to be recent developments [
https://doi.org/10.1021/acs.jctc.7b00067] (top result in a google search)
Best,
Matias
----- Mensaje original -----
De: "Alessandro LANDI" <alelandi1.unisa.it>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Martes, 16 de Julio 2019 8:11:14
Asunto: [AMBER] Recent Force Fields for nucleotides
Dear all,
I am currently performing molecular dynamics simulations on DNA single and
double strands in water. Unfortunately, I am using a quite old version of
both Amber and AmberTools suite, therefore I am considering buying the
latest version.
However, as a newbie, I would like to get information about the most
up-to-date force field to be used for the DNA and, in particular, if there
are any polarizable force fields to be used when simulating DNA sequences.
I have read about some recent force fields (e.g. ff12pol, even though, to
the best of my knowledge, it has not been yet implemented in Amber18), but
I have not been able to understand if they could be used only for peptydes,
or if some of them has been parametrized also for DNA.
Can you please provide me some information about the available force fields
for DNA in Amber18 and if they are polarizable?
Thanks in advance,
Alessandro
--
Alessandro Landi, Ph.D. Student
Dipartimento di Chimica e Biologia "Adolfo Zambelli"
Università degli Studi di Salerno
Via Giovanni Paolo II, 132 - 84084 - Fisciano (SA)
Phone number 089969390
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Received on Tue Jul 16 2019 - 09:00:02 PDT
