ok, I thought RMSd was from ideal dihedral angles, since that was the
restrain i fixed... thanks! (however, even if it only deals with valence
angles, would you think it's acceptable?)
sorry I wasn't very clear in my second question. It may be a trivial
question...however, in my second run, I had, for example, for VAL an output
of j=7.6Hz (that was very near to my observed averaged j). This corresponds
to a dihedral phi of about -85°. But when I measured it on my pdb it was
about -145°. I believe that this means that I am measuring theta (85+60) not
phi. Therefore, there is something wrong, if I am measuring a j which should
give me a phi of 85°, yet I am calculating 145.° Could it be related to the
j being averaged or not ? I assumed that the j in the output is not
averaged, but is precisely related to the "final" molecule, therefore, it
should be the precise conformation with that dihedral angle.
2010/11/3 case <case.biomaps.rutgers.edu>
> 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
>
> --
>
> ================================================================
> 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 - 09:30:03 PDT
