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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Received on Thu May 28 2020 - 06:00:02 PDT
