[AMBER] pulling along RMSD

From: Qinghua Liao <scorpio.liao.gmail.com>
Date: Wed, 1 Nov 2017 13:07:06 +0100


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 - 05:30:07 PDT
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