Dear Amber Users,
I am using ptraj quasi harmonic analysis to calculate the entropy.
With reference to an average pdb file of the entire structure, I specify
the
number of ligand and receptor residues in the complex.
reference avg.pdb pdb
rms mass reference :1-100
matrix mwcovar name com-var :1-100
analyze matrix com-var out com-cov thermo reduce
I get the warning as
warning: setting vibrational entropy to zero for mode 10975 with vtemp =
-258451981.
temperature 298.150 kelvin
pressure 1.00000 atm
molecular mass (principal isotopes) 59541.73700 amu
principal moments of inertia (nuclei only) in amu-A**2:
6918814.75 16355115.56 18081675.89
rotational symmetry number 1.
Warning-- assumption of classical behavior for rotation
may cause significant error
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total *********** -nan 11211.514
translational .888 2.979 57.502
rotational .888 2.979 55.643
vibrational *********** -nan 11098.369
Is this something to do with the structure. These values are calculated
twice.
Is this for the entire complex.
Thanks
Kirtana
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Received on Sun Sep 29 2013 - 17:30:03 PDT
