On Thu, 2014-04-24 at 18:04 +0800, Neha Gandhi wrote:
> Hi List,
>
> I am not an NMR expert, so apologies for ignorance.I want to acheive the
> following " the NOE between the Gly207 HN and Ser208 HN is strong, so
> imposing a harmonic constraint on it with a energy penalty = zero when the
> distance is between 2 and 3.5Angstroms, and then a quadratic term when it
> goes beyond this value. Secondly, the contact between the methyl carbon of
> the pThr205 and the Gly207 HN is weak, so restraining this distance to 6
> Angstroms"
>
> Is my syntax in .RST file correct? Your feedback is appreciated. Is there a
> way to apply energy penalty when using distance restraints (such parameter
> is present in chemical shift restraint in amber i think).
>
> #( proton 1 proton 2 upper bound)
> #---------------------------------------------
> #
> # 17 GLY H 18 SER H 3.50
> #
> &rst iat= 199, 206, r3= 3.50, r4= 4.00,r1 = 2.0, r2 = 2.5, rk2=0.0,
> rk3=20.0, &end
> #
> # 15 TPO CG2 17 GLY H 6.00
> #
> &rst iat= 173, 199, r1= 2.00, r2= 2.50, r3= 6.00, r4= 6.50, &end
> #
>
This restraint specification looks like it does what you described. The
best advice I can give is to try it out and then compare the restraint
energies that sander or pmemd prints out with values that you compute by
hand for a couple of frames to make sure they match.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 24 2014 - 05:00:02 PDT
