[AMBER] huge values for the vibrational entropy from ptraj

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Tue, 29 Oct 2013 09:56:31 +0100

Dear all,

I did an entropy estimation from a quasi harmonic analysis in ptraj of a
150 ns simulation (50.000 frames). I get huge numbers for the
vibrational entropy (sample output below).
Now, if I do it in the MMPBSA context (dS=dScom-dSrec=dSlig), I get a dS
= - 2.3 kcal/mol*K which makes a TdS = 698 kcal/mol ..

Well, to me, this is outrageous ... But as I am relatively new to the
method, I am wondering if this is maybe expected due to lack of
convergence or other issues with the method ... Or maybe is my system
that is problematic ? Has anybody experienced such huge values ?

Thanks for any insights

Best wishes
Vlad

P.S. ptraj from Amber Tools 13 ...



-------------- sample output complex---------------------------
            freq. E Cv S
           cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
  Total *********** NaN 20143.554
  translational 0.888 2.979 58.245
  rotational 0.888 2.979 62.384
  vibrational *********** NaN 20022.926


------------------sample output receptor ----------------------------
            freq. E Cv S
           cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
  Total *********** NaN 12507.904
  translational 0.888 2.979 56.955
  rotational 0.888 2.979 61.173
  vibrational *********** NaN 12389.776


--------------------sample output ligand ----------------------------------
             freq. E Cv S
           cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
  Total 76110.251 NaN 9978.670
  translational 0.888 2.979 55.130
  rotational 0.888 2.979 57.396
  vibrational 76108.475 NaN 9866.143



-------------------- sample input --------------------------
trajin _MMPBSA_complex.nc 10000 50000 5
rms mass first :1-307
matrix mwcovar name comp.matrix :1-307
analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo reduce
rms mass first :153-307
matrix mwcovar name rec.matrix :153-307
analyze matrix rec.matrix out _MMPBSA_receptor_entropy.out thermo reduce
rms mass first :1-152
matrix mwcovar name lig.matrix :1-152
analyze matrix lig.matrix out _MMPBSA_ligand_entropy.out thermo reduce


-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 29 2013 - 02:00:03 PDT
Custom Search