Hi John,
Thank you for your reply. That is exactly what I have asked. And the reason for
this question is that I don't see the difference in CARB energy term if I
change the potential from harmonic to square. The energy is very high
(~9000-10000). I am using the script from mef-dna example (sa_mef_dipo.inp) Is
there some other parameters I have to change?
Thank you,
Irina.
----- Original Message -----
From: John Kuszewski
To: Irina Nesmelova
Cc: xplor-nih at nmr.cit.nih.gov
Sent: Thursday, January 17, 2008 4:37 PM
Subject: Re: [Xplor-nih] carbon chemical shift error
Hi,
I presume you're asking about the CARBonshift energy term.
Do you mean you want to define an error in your observed Ca or Cb chemical
shifts? If so, you can't. The term's accuracy in predicting carbon shifts
from backbone torsion angles is rather low (~ 1ppm, if I remember correctly)
compared to the accuracy of measurement of Ca and Cb chemical shifts, so
there's no point in defining a squarewell that way.
Rather, the carbonshift's squarewell potential works by comparing the
difference between observed and expected shift values relative to the known
accuracy of the prediction surface at each point. These accuracies are
recorded in the same table as the expected secondary chemical shifts.
So all you need to do is turn on the square well potential shape by calling
CARBon SQUArewell, and you're all set.
If I've misunderstood your question, forgive me.
--JK
On Jan 17, 2008, at 5:00 PM, Irina Nesmelova wrote:
Hello,
How can I input the error for carbon chemical shift?
Thank you,
Irina.
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