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
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Received on Tue Oct 29 2013 - 02:00:03 PDT
