Hi Christina,
Thanks a lot for the insight and script! That more or less covers for what
I wanted to do NOE and CSP wise, and LAMORD should more or less fill in the
gap that the protein CSP softwares I found weren't able to do.
Best,
Kenneth
On Thu, May 28, 2020 at 8:42 AM Christina Bergonzo <cbergonzo.gmail.com>
wrote:
> Hi Kenneth,
>
> I do not know of any stand alone tools that will calculate NMR observables
> from a trajectory.
> I regularly do this without too much hassle using a combination of bash/awk
> scripting and Cpptraj/shifts.
> I also back out NOE distances from distance restraints - if you want to
> predict NOEs using a trajectory, that's a different question (see Henriksen
> et al. JPCB, dx.doi.org/10.1021/jp400530e), but also distance based.
>
> If you look at the Cpptraj distance command, there is an option for
> evaluating a distance as an NOE.
> I write a script that takes my atoms of interest from whatever experimental
> file format I have, and formats them into the distance command:
>
> distance d0 :1.H1' :1.H4' type noe bound 0.0 bound 7.0 out
> dist/noe.val.0.dat
> ....
> distance d50 :6.H5'' :6.H6 type noe bound 0.0 bound 7.0 out
> dist/noe.val.50.dat
> analyze statistics all out noe.dat
>
> The last part dumps analysis of each distance into a file (noe.dat)
> containing initial and final values, avg and standard deviation, 1/r^6
> averages, # of violations, etc.
> Example output:
>
> STATISTICS :1.H1' and :1.H4'
> AVERAGE: 3.0492 (0.2559 stddev)
> INITIAL: 3.0944
> FINAL: 3.2662
> NOE SERIES: S < 2.9, M < 3.5, W < 5.0, blank otherwise.
> |SMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM|
> NOE < 7.00 for 100.00% of the time
> NOE <r^-6>^(-1/6)= 2.9650
> #Violations: Low= 0 High= 0 Total= 0
> Rexp= 7.0000 <Violation>= -4.0350
>
> < 2.5 2.5-3.5 3.5-4.5 4.5-5.5 5.5-6.5 > 6.5
> -------------------------------------------------------
> %occupied | 2.4 | 95.1 | 2.5 | | | |
> average | 2.402 | 3.051 | 3.611 | | | |
> stddev | 0.084 | 0.223 | 0.103 | | | |
> -------------------------------------------------------
> __________________________________________________________________
>
> For chemical shifts for nucleic acids, I use shifts for protons, and
> there's larmor-D for proton and carbon shifts.
> And, I go through a similar procedure, where I look at the experiment to
> see what's be deposited, use shifts to calculate those values from PDBs (I
> have found you'll need to rename 5' and 3' ends to their non-terminal
> counterparts i.e., C3 to C), and then calculate for each frame and average.
>
> Good luck!
> -Christina
>
> On Wed, May 27, 2020 at 7:48 PM Kenneth Huang <kennethneltharion.gmail.com
> >
> wrote:
>
> > Hi all,
> >
> > A general question- does anyone know of tools (assuming there isn't a
> > combined suite) for calculating CSP or NOEs from a trajectory? I know
> > there's SPARTA+ and shiftX2 for protein CSPs for proteins, but with DNA
> all
> > I've seen is the NMR option in Gaussian, which seems prohibitively
> > expensive.
> >
> > Likewise for NOEs I know of MD2NOE but haven't ever used it in context of
> > DNA, and other than back-calculating from the distance restraints, I was
> > just wondering if there had been any other options in cpptraj?
> >
> > Best,
> >
> > Kenneth
> > --
> > Ask yourselves, all of you, what power would hell have if those
> imprisoned
> > here could not dream of heaven?
> > _______________________________________________
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> >
>
>
> --
> -----------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> Biomolecular Measurement Division, MML, NIST
> -----------------------------------------------------------------
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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here could not dream of heaven?
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Received on Thu May 28 2020 - 21:00:02 PDT
