Hi Ilyas,
just came back from a summer vacation. Thank you for responding.
I have a 7nt-loop RNA hairpin structure that I synthesized in my
laboratory. It has a nucleotide residue derivative for which I developed my
own force field parameters, and I have been currently testing the new
parameters to see if they are consistent with our NMR data.
I have performed a histogram analyses. I think the problem resides
somewhere else. It appears that there is a glitch in our server..
Now, the problem seems to be solved.
Best,
Cenk
On Sat, Aug 20, 2022 at 12:54 AM Ilyas Yildirim <iyildirim.fau.edu> wrote:
> Which force field are you using? Also, is this a regular RNA sequence? We
> also observe alfa ~ 60 sometimes but not all the time. Why don't you
> analyze the trajectory and perform a histogram analyses (maybe in 2D;
> alfa/gamma)? It should point out what the most observed population(s) are
> for alfa/gamma.
>
> Best regards,
>
> Ilyas Yildirim, Ph.D.
> ---------------------------------------------------------
> = Assistant Professor =
> = Department of Chemistry & Biochemistry =
> = Florida Atlantic University =
> = 5353 Parkside Drive, Jupiter, FL 33458 =
> = Building MC17, Room # 224 =
> = Phone: +1(561)799-8325 | E-mail: iyildirim_at_fau.edu =
> ---------------------------------------------------------
> = Website: https://cescos.fau.edu/~iyildirim/ =
> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
> ---------------------------------------------------------
> ------------------------------
> *From:* Cenk Andac <cenkandac.gmail.com>
> *Sent:* Friday, August 19, 2022 5:34 PM
> *To:* Ilyas Yildirim <iyildirim.fau.edu>
> *Cc:* Daniel Roe <daniel.r.roe.gmail.com>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] CPPTRAJ: sign convention for dihedral angles!!
>
> *EXTERNAL EMAIL : *Exercise caution when responding, opening links,
> or opening attachments.
>
>
> Opps... this is to correct a typo in my previous mail
> " I understand that even though one of the nucleotides in dsRNA structure
> adopt g+ conformer in the alpha torsion, it will not necessarily distort
> the nature of A-RNA. "
>
>
> On Sat, Aug 20, 2022, 12:11 AM Cenk Andac <cenkandac.gmail.com> wrote:
>
> Hi Ilyas,
> Thank you for having an additional thought in the discussion.
> I understand that even though one of the nucleotides in dsRNA structure
> adopt g- conformer in the alpha torsion, it will not necessarily distort
> the nature of A-RNA.
> What really surprises in my case is that all of the nucleotide residues in
> dsRNA adopt g+ conformers in the alpha torsion, and yet it is an A-RNA.
> and that all manually measured alpha torsions point to g- conformer.
> I just cant make sense out of this.
>
> Best,
>
> Cenk
>
> On Fri, Aug 19, 2022, 11:31 PM Ilyas Yildirim <iyildirim.fau.edu> wrote:
>
> In the simulations you will see a residue having an alfa ~ 60 (or 180 - I
> am not sure about the region) and gamma ~ -60, which will not distort the
> A-form geometry that much. It does not mean that, however, this is the
> expected intrinsic behavior of RNA. We have revised the alfa and gamma
> torsional parameters for RNA recently, which produce the expected
> alfa/gamma behavior.
>
> Wales, D. J., and *Yildirim, I.**, "Improving Computational Predictions
> of Single-Stranded RNA Tetramers with Revised α/γ Torsional Parameters for
> the Amber Force Field", *J. Phys. Chem. B* 121, 2989-2999, *2017*.
>
> Check out the alfa and gamma profiles we discuss in the paper, which are
> different than the predictions with amber10 parameters.
>
> Ilyas Yildirim, Ph.D.
> ---------------------------------------------------------
> = Assistant Professor =
> = Department of Chemistry & Biochemistry =
> = Florida Atlantic University =
> = 5353 Parkside Drive, Jupiter, FL 33458 =
> = Building MC17, Room # 224 =
> = Phone: +1(561)799-8325 | E-mail: iyildirim_at_fau.edu =
> ---------------------------------------------------------
> = Website: https://cescos.fau.edu/~iyildirim/ =
> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
> ---------------------------------------------------------
> ------------------------------
> *From:* Cenk Andac via AMBER <amber.ambermd.org>
> *Sent:* Friday, August 19, 2022 4:19 PM
> *To:* Daniel Roe <daniel.r.roe.gmail.com>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] CPPTRAJ: sign convention for dihedral angles!!
>
> Hi Dan,
> Thank you for responding.
> I have an MD trajectory for A-RNA double helix. I have gone through may of
> the frames and computed alpha torsions manually via UCSF Chimera, they are
> all around ~ 60o (gauche -). In A-RNAs with WC base pairs, alpha torsions
> should adopt g- conformer according to the table below, I think.
>
> [image: image.png]
> Arnott, S. (1999). In Oxford Handbook of Nucleic Acid Structure (Ed.
> Neidle, S.), p. 1, Oxford University Press,
> Oxford.
>
>
> Having said that I now am quite confused with the stat output I previously
> mentioned. It says the average alpha torsion is around +60o while I
> manually measured -60o (minus for counterclockwise torsions)
>
> Do you have any idea as to what I am missing here!!
>
> Best,
>
> Cenk
>
>
> On Fri, Aug 19, 2022, 5:30 PM Daniel Roe via AMBER <amber.ambermd.org>
> wrote:
>
> > Hi,
> >
> > On Fri, Aug 19, 2022 at 3:32 AM Cenk Andac via AMBER <amber.ambermd.org>
> > wrote:
> > >
> > > STATISTICS G2-alpha
> > > AVERAGE: 65.8043 (10.0676 stddev)
> > > INITIAL: 64.6928
> > > FINAL: 57.9292
> >
> > A torsion value of 65 deg. is almost right in the middle of what by
> > convention is considered gauche+ (between 30 and 90 degrees), so
> > everything seems correct. Why do you think this is a bug?
> >
> > -Dan
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Sat Sep 03 2022 - 07:30:03 PDT
