Re: [AMBER] protein && DNA in implicit solvents

From: Carlos Simmerling <>
Date: Wed, 1 Nov 2017 10:31:57 -0400

we did some tests in our paper on the GBneck2 model for nucleic acids. Keep
in mind, though, that energy/force calculations for big systems with
implicit water can actually be more computationally demanding than in
explicit water. Carefully benchmark your system to find out.

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic
Acids and Their Complexes with Proteins
Nguyen, H., PĂ©rez, A., Bermeo, S., Simmerling, C., Journal of Chemical
Theory and Computation, 2015, 11 (8), 3714-3728
DOI: 10.1021/acs.jctc.5b00271
PMCID: PMC4805114

On Wed, Nov 1, 2017 at 8:15 AM, Qinghua Liao <> wrote:

> 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,
> Qinghua
> Hello,
> 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,
> Qinghua
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Received on Wed Nov 01 2017 - 08:00:02 PDT
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