On Tue, Feb 19, 2013, Rasha Alqus wrote:
>
> Am trying to calculate the vibrational frequency of a compound in
> vacuum using normal mode analysis, am using Amber 11 and am confused on
> how to do it using: nmode or mmpbsa_py_nabnmode or using NAB ( Second
> derivatives and normal modes) programs.
Either nmode or NAB should be fine for a project like this. [Note that the
quality of the results will depend on the quality of the force field you use,
and that the Amber force fields (for example) are not optimized for vacuum, or
for the computation of vibrational frequencies.]
....dac
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Received on Tue Feb 19 2013 - 10:00:02 PST
