I am using 5000 frames and the residues 1-100 contains 5599 atoms.
The ligand has 2595 and receptor has 3004 atoms.
Regards
Kirtana
On Mon, Sep 30, 2013 at 11:59 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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 - 11:00:05 PDT
