[AMBER] entropy

From: kirtana S <skirtana4.gmail.com>
Date: Sun, 29 Sep 2013 20:17:07 -0400

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
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 =

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
Is this for the entire complex.

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Received on Sun Sep 29 2013 - 17:30:03 PDT
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