I believe it is in Amber 15 as well, Hai can confirm...
On Wed, Jun 29, 2016 at 11:04 AM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 29 2016 - 09:00:02 PDT
