Why the NMA discrepancies?

From: Jones de Andrade <johannes.titus.phy.qub.ac.uk>
Date: Mon, 17 Mar 2003 01:09:16 +0000 (GMT)

        Hi everybody.

        I was just wandering whether am I making any mistake or there is
this difficult. I was doing some tests on the model for the benzene
molecule, when I came across with the fact that even such a simple
molecule can give odd results when comparing the FF NMA results and the
scalled QM NMA results. We can find some strong differences, sometimes of
about more than 100 cm-1, what for would not make sense for this simple
molecule (since isn't exactly the benzene molecule the one used to develop
the parameters for the CA and HA atoms and bonds, angles and dihedrals?).
I'm asking because unless I'm using the amber force field and the resp
calculated charges, I don't use the amber package programs. So, maybe
there is a problem in the program or in the input, but, since it
reproduced quite well the other published NMAs from amber, it should be
fine. Has anyone, so, already tested a simples molecule like the benzene
and saw if it could reproduce the correct NMA data?

                        Thanks a lot,

Received on Mon Mar 17 2003 - 01:53:00 PST
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