> On Jun 29, 2016, at 11:47 AM, Kasprzak, Wojciech (NIH/NCI) [C] <kasprzaw.mail.nih.gov> wrote:
>
> Hai, Carlos,
>
> Thank you again. I will pass this information to our software managers, as I am not sure
> which updates have been implemented in the Amber 14 that we have.
If you are using updated amber14, make sure you can see gb_alpha_hnu (and so on) in your mdout file.
> I'll read the paper ASAP. Is there a new tutorial for the Implicit Solvent with NA,
> or is it a matter of updated forcefield params that work better with the protocol
> I've been using (Langevin ntt=3, etc)?
>
There is no special tutorial for this since it is just matter of updating FF params like you said. You just need to specify igb=8 and use mbondi3. We have detail in the paper.
Cheer
Hai
> 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
>
> ________________________________________
> From: Nhai [nhai.qn.gmail.com]
> Sent: Wednesday, June 29, 2016 11:37 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids
>
> 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 - 09:30:03 PDT
