[AMBER] protein && DNA in implicit solvents

From: Qinghua Liao <scorpio.liao.gmail.com>
Date: Wed, 1 Nov 2017 13:15:26 +0100

Hello again,

Amber ff14SB and Amber DNA bsc1 force fields are used for the protein
and the DNA of the complex, respectively, and the complex system with
water is very big.

I am thinking of performing the simulations in implicit solvents
(following simulations with explicit water will also be performed),
but I have no experience on it before. Is there someone who did some
tests? Any comments or suggestions? Thanks a lot!

All the best,


I have a complex of a protein and a DNA, and the binding is stable. I am
planning to do
some pulling simulations along a RMSD, which will be calculated based on
the heavy atoms of the
DNA after the alignment of the protein. The Amber ff14SB and DNA bsc1
force fields were chosen
for the protein and DNA, respectively. The purpose of the simulations is
to pull the DNA out of the initial binding, and it might
find another binding during the pulling. Could someone give me some tips
on how to set it up with AMBER?
Thanks a lot!

All the best,

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Received on Wed Nov 01 2017 - 05:30:08 PDT
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