Re: AMBER: need help to calculate IR spectra from amber trajectory

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Thu, 10 May 2007 15:16:59 -0400

S.Sundar Raman wrote:
> dear amber friends,
> i would like to calculate IR spectra for amide I using amber trajectory. i
> simulated a peptide using sander in amber9. i would like to calculate the
> N-H frequency for various amides present in my peptide. is it possible to
> calculate using ptraj? please explain the procedure in detail. it will be a
> great help for me and i am eagerly waiting for reply from amber groups.
> thank you
Dear Sundar,
If I could offer my two cents, do not even try to do this!

There are basically at least two ways of doing what you want:

1. read on the calculation of IR spectra using dipole-dipole correlation
functions.
2. Compute normal modes for the system.

However, there is NO way that a classical force field will give you good
results on this !

You will get some rough estimates, but the fixed charge model cannot
possibly reproduce experimental frequencies.

Look at work by Krimm et al on this, or some papers by Angel Garcia on
computing IR spectra on peptides.

Now, if you are willing to use QM/MM methods, then things look much better.

Cheers
a. 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Sun May 13 2007 - 06:07:28 PDT
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