AMBER Archive (2007)

Subject: AMBER: entropy with ptraj

From: Marius Retegan (marius.s.retegan_at_gmail.com)
Date: Mon Oct 08 2007 - 07:24:36 CDT

Hello,
I'm trying to use ptraj to calculate the entropy for o small ligand
from a dcd trajectory.
I've used the following input
================================
trajin inhibitor.dcd
rms first *
matrix mwcovar name mwcvmat
analyze matrix mwcvmat thermo reduce
go
================================
If I align the structures using rms first * I get high energy for the
last 6 frequencies If I don't do the alignment the last 6 modes are
not equal to zero and the other modes are changed and I get a
different value for the entropy.
>From what I've read on the amber list this alignment is done so that
the rotational and translational modes are set to zero.
So my question is what am I doing wrong?
================================
            freq. E Cv S
          cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
 Total 340383.423 NaN 164.885
 translational 0.888 2.979 44.344
 rotational 0.888 2.979 35.646
 vibrational 340381.646 NaN 84.895
     1 15.907 0.592 1.985 7.083
...
    63 1810.534 2.589 0.024 0.003
    64********** 6657.325 NaN 0.000
    65********** 26253.291 NaN 0.000
    66********** 61634.738 NaN 0.000
    67********** 211077.383 NaN 0.000
    68********** 26078.713 0.000 0.000
    69********** 8603.003 0.000 0.000
================================
I've attached to output from ptraj one with alignment and one without.
Thank you
Marius


  • application/octet-stream attachment: align.out

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