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

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Thu, 3 Oct 2019 23:37:51 -0700

Those smaller magnitudes also match this 2014 paper on B DNA:

https://pubs.rsc.org/en/content/articlehtml/2014/ob/c4ob00427b

But note that the difference, 5 Kcal/mol is the same. It might apply
here that for molecular energies within a simplified force field,
absolute accuracy isn't valued as highly as discriminative accuracy,
i.e. one only looks at the deltas between conformational energies of a
given molecule or set thereof. I don't know the claims of the unnamed
code you are using, but that's a stock answer that might apply. :-)

Bill

On 10/3/19 11:20 PM, Swagata Halder wrote:
> 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
> _______________________________________________
> 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 Fri Oct 04 2019 - 00:00:02 PDT
Custom Search