AMBER Archive (2003)

Subject: RE: Why the NMA discrepancies?

From: Yong Duan (yduan_at_udel.edu)
Date: Sun Mar 16 2003 - 21:46:57 CST

Dear Andrade:

Can you be more specific?

Could the difference you observed be the consequence of different
solvation environment? The reason for using RESP charges is that they
mimic condensed phase electrostatics, rather than typical gas phase. I
would anticipate difference if your QM NMA is done in gas phase.
Nevertheless, I would be interested in knowing the detail of your
comparison.

yong

-----Original Message-----
From: Jones de Andrade [mailto:johannes_at_titus.phy.qub.ac.uk]
Sent: Sunday, March 16, 2003 8:09 PM
To: amber_at_heimdal.compchem.ucsf.edu
Subject: Why the NMA discrepancies?

        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,

                                                        Jones