Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop

From: Jiri Sponer <sponer.ncbr.muni.cz>
Date: Fri, 4 Oct 2019 09:55:12 +0200 (MEST)

Yes, these QM numbers are correct.

For the latest QM benchmark and comparison with the AMBER force field see:
Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking
Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00643

also
Can We Accurately Describe the Structure of Adenine Tracts in B-DNA?
Reference Quantum-Chemical Computations Reveal Overstabilization of
Stacking by Molecular Mechanics
https://pubs.acs.org/doi/10.1021/ct3001238

The MM AMBER numbers should be similar to the QM benchmarks within very
few kcal/mol, usually slightly overestimated. Due to slide and roll
typical A-form stacking should be slightly weaker than B-DNA stacking
(plus the effect of T vs U).
  If there is a
larger difference, there must
be some technical glitch in the MM computations.
Try to see separately the vdW and elstat. terms.
-40 or -35 kcal/mol between two stacked base pairs is definitely
unrealistic.

Best wishes, Jiri
-------------------------------------------------------
Jiri Sponer
Institute of Biophysics of the Czech Academy of Sciences
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer.ncbr.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/
https://www.ibp.cz/en/research/departments/structure-and-dynamics-of-nucleic-aci
ds/info-about-the-department
-----------------------------------------------------------



On Fri, 4 Oct 2019, Swagata Halder wrote:

> Date: Fri, 4 Oct 2019 06:20:45 +0000
> From: Swagata Halder <swagatah.iisc.ac.in>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG
> tetra loop
>
> HI,
>
> Thanks for your quick reply. My expectations for GC/GC step and AU/AU step are near about -14 Kcal/mol and -9Kcal/mol respectively. Stacking energies which I got from pair wise analysis are higher compared to other standard reference values ( Daniel et al. Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps
> in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations? J. Phys. Chem. B 2010, 114, 11911203). Yes, I am using canonical tetraloop structure.
>
>
> Regards,
> Swagata Halder
> Indian Institute of Science.
>
>
>
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: Thursday, October 3, 2019 2:39 PM
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop
>
> What are your expectations, and what are they based on? Are you using a
> canonical tetraloop structure?
>
> Bill
>
> On 10/3/19 12:58 AM, Swagata Halder wrote:
>> Hi all,
>>
>> I am calculating stacking energy of a RNA containing UUCG tetraloop by cpptraj pair wise command (Amber 18). Unfortunately I got some higher value than expected. As a example for GC/GC step I got -40Kcal/mol and for AU/AU step , got -35Kcal/mol. Please suggest me if anything is going wrong for the calculation.
>>
>>
>> Thanks in advance.
>>
>> Regards,
>> Swagata Halder
>> Indian Institute of Science
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 04 2019 - 01:00:02 PDT
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