Carlos,
Thank you for the quick answer an the pointer to the paper I missed. I am waiting for Amber 16
to get installed in our computer center. Sounds exciting!
Thank you very much, Voytek Kasprzak
------------------------------------------------------------------------------------------------------
From: Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: Wednesday, June 29, 2016 10:33 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids
you should take a look at our recent work on this, it has optimized
parameters for nucleic acids as well as many validation examples. It is
implemented in Amber 16. We have ongoing work to further improve the model,
but this might do what you need already.
Refinement of Generalized Born Implicit Solvation Parameters for Nucleic
Acids and Their Complexes with Proteins
Nguyen, H., Pérez, A., Bermeo, S., Simmerling, C., Journal of Chemical
Theory and Computation, 2015, 11 (8), 3714-3728
DOI: 10.1021/acs.jctc.5b00271
Carlos
On Wed, Jun 29, 2016 at 10:22 AM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
> Dear Amber Users,
>
> Every few years I try to revisit the implicit solvent MD for use with our
> fairly large RNA & DNA-based
> nanostructures (300+ nucleotides). Think of a cube with edges made of
> A-form (RNA) or B-form (DNA)
> helices and linked in the corners with single-stranded bridges. All
> helical edges are fully paired by design.
> Some of the edges contain the 5'-3' breaks in the middle (i.e. one side
> is connected with the standard
> backbone, the other held in place by stacking interactions).
>
> I am evaluating a Langevin protocol in Amber 14 (ff14SB, igb=1, ntt=3,
> gamma_ln=1.0,
> offset=? (0.09 or 0.13) and saltcon=1.0) for such cubes (PBradii mbondi
> used in Leap).
>
> DNA cubes experience distortions larger than in the explicit solvent
> simulations, but generally
> maintain structural integrity, whereas RNA-base cubes show a tendency to
> lose the stacking
> in the middle of the helices across the 5' - 3' breaks, and I see a
> rotation of the initially stacked
> nucleotides away from each other (up to 180'). G-C|G-C or G-C|C-G
> combinations hold with some
> distortions, but G-C|A-U or G-C|U-A tend to "twist open" (| - indicates
> backbone connection).
>
> Questions:
> 1) Are there any new options/parameters for Implicit Solvent MD -
> something equivalent to the
> Liu ae al. (A Novel Implicit Solvent Model...), Biophys J, 2013
> implemented in an unfortunately
> named STINKER?
>
> 2) I've been relying on the default offset (0.09) in the runs so far. I
> am evaluating 0.13. Should it
> help with the described problem in RNA?
>
> 3) Setting gbsa=1 slows down the simulation speed well below that of the
> explicit solvent MD.
> Is it expected or is it a sign of something seriously wrong? A
> flexing object like a cube may
> experience more surface area changes than a simple duplex, and the
> question in my mind is if
> ignoring it (gbsa=0) is justified. The calculated values appear to
> be ~ 0.5% of the total Energy.
>
> 4) Are other parameters more important than those mentioned above? I am
> using dt=0.002, for example.
>
> If you have any suggestions or comments, I would appreciate them very much.
>
> Best regards, Voytek Kasprzak
>
> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer,
> Basic Science Program,
> Leidos Biomedical Research, Inc.
> Frederick National Laboratory for Cancer Research (FNLCR)
> Frederick, MD 21702
> (301) 846 5537
> http://binkley2.ncifcrf.gov/users/kasprzak
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>
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Received on Wed Jun 29 2016 - 08:30:03 PDT
