Yeah. Jason made a patch for amber14 last year.
http://ambermd.org/bugfixes/14.0/update.12
Hai
> On Jun 29, 2016, at 11:29 AM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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
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Received on Wed Jun 29 2016 - 09:00:03 PDT
