AMBER Archive (2007)

Subject: AMBER: Chemical shift: simulation vs. experiment

From: Mingfeng Yang (mfyang_at_gmail.com)
Date: Thu May 03 2007 - 20:07:05 CDT

Dear fellows,

This topic might not be so relevant to Amber. But I do need a little
help from our community, since I can barely find anyone to discuss with
me right now.

I finished a MD simulation done by Amber9, igb=7, PARM99SB force fields,
and tried to compare the results with experiment. Below is what I did:

I took an ensemble average of the chemical shift values of N, CA, CB
which were calculated by Dr. Case's SHIFTS program, and compared with
the corresponding chemical shifts determined by solution state NMR.

Encouragingly, for CA and CB atoms, the correlations between simulation
and experiment are nearly 1 (>0.995). The correlation for N atoms are
0.877 which I consider still pretty decent, but the N chemical shifts
are smaller than experimental values by 5.

Can anybody explain the difference of N chemical shifts between
simulation and experiments?

Do you consider the comparison fair, and the results be encouraging?

Thanks,
Mingfeng

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