Dear Amber Users,
For a test I calculated vibrational modes
of a single water molecule by MMPBSA.py. There is a WAT unit in xleap
and the inpcrd and prmtop file is generated form that. Then I run
MMPBSA.py using the following input file-
normal mode calculation
&general
startframe = 1,
endframe = 1,
/
&nmode
nmode_igb = 0
/
The vibrational normal modes obtained from here are
bending = 1996.938 cm^-1
symmetric stretch= 3735.841 cm^-1
antisymmetric stretch = 5952.802 cm^-1
But in literature I have seen that the last two frequencies in gas phase are
symmetric stretch = 3657 cm^-1
antisymmetric stretch = 3756cm^-1
So, here the difference is significant.
I tried it in quantum mechanical software TURBOMOLE. Here also I used
same initial coordinates. The result is good here.
bending = 1642.33 cm ^-1
symmetric stretch = 3651.30 cm^-1
antisymmetric stretch = 3754.15cm^-1
So, what wrong am I doing? What should I do? Please help
Sanjib
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Received on Mon Sep 24 2012 - 04:30:02 PDT
