Hi,
How many frames are you using to calculate the covariance matrix, and
exactly how many atoms are in the mask ':1-100'?
-Dan
On Sun, Sep 29, 2013 at 6:17 PM, kirtana S <skirtana4.gmail.com> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Sep 30 2013 - 09:00:06 PDT
