On Wed, Nov 03, 2010, Rossella Noschese wrote:
> Hi, I'm a new user of amber(in my university we only have license for
> amber7). I tried to run a restrained simulated annealing of a peptide.
> 1) I extracted my J(HNCalphaHalpha) values (J for ILE:8.06Hz; J for
> VAL:7.56Hz) from my spectra and I added these restraints to my run.
> First I used rjcoef A=6.4 B=-1.4 C=1.9 and rk2=rk3=32 and this was my
> output:
>
> H VAL 2 -- HA VAL 2: 6.899 7.400 0.501 8.017 j
> H ILE 7 -- HA ILE 7: 6.900 7.900 1.000 32.000 j
> Total distance penalty: 0.850
> Total torsion penalty: 40.017
> | RMS deviation from ideal bonds : 0.0166
> | RMS deviation from ideal angles: 2.898
>
> with a too large RMS deviation!!
Why do you think this is too large? Note that the "RMS deviation from
ideal angles" is for valence angles (two atoms each bonded to a common
third atom); it has nothing to do with torsion angles that are related to
J-coupling restraints. Note also that J(H-Ha) coupling constants of 8.1
and 7.6 Hz don't really have much information content: lots of different
conformations (phi torsion angles) could be present, averaging out to the
observed, intermediate value.
> 2) When I look at my pdb file my restrained dihedrals seem to be calculated
> on teta instead of phi angles ( 3J=6.4cos2θ-1.4cosθ+1.9 with θ=φ-60°) , am
> I right? How can I have my dihedral from j value calculated on phi angles?
I don't understand the question. Theta is just an intermediate quantity in
the calculation: phi -> theta -> J.
....dac
--
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David A. Case | email:
BioMaPS Institute and Dept. of | case.biomaps.rutgers.edu
Chemistry & Chemical Biology | fax: +1-732-445-5958
Rutgers University | phone: +1-732-445-5885
610 Taylor Rd. |
Piscataway, NJ 08854-8087 USA | http://casegroup.rutgers.edu
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Received on Wed Nov 03 2010 - 08:00:02 PDT
