Use the total to find the entropy value.
I tried to calculate the entropy effect for the protein which I am working
on, it couldn't work and failed. I got problem in minimization. Would you
please send me your input file to compare with mine?
Regards,
Dima
-----DeChang Li <li.dc06.gmail.com> wrote: -----
To: amber.ambermd.org
From: DeChang Li <li.dc06.gmail.com>
Date: 10/18/2010 09:44AM
Cc: li.dc06.gmail.com
Subject: [AMBER] The result of entropy calculation
Dear all,
I used NMODE module of AMBER 8 to calculate the entropy contribution
of
my system, following MM/PBSA method. The following is one of my result.
Does
this result normal? And which value should I used to calculate the
entropy -T*S, the Total one (7534.636), or the vibrational one (7421.937)
only?
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------
------
Total 18218.711 6311.488 7534.636
translational 0.888 2.979 55.783
rotational 0.888 2.979 56.916
vibrational 18216.935 6305.531 7421.937
1 0.000
2 0.000
3 0.000
4 0.000
5 0.060
6 0.075
7 2.992 0.592 1.986 10.400
8 3.622 0.592 1.986 10.021
9 4.111 0.592 1.986 9.769
10 4.839 0.592 1.986 9.446
11 4.987 0.592 1.986 9.386
12 5.731 0.592 1.986 9.110
13 6.065 0.592 1.986 8.997
14 6.172 0.592 1.986 8.963
15 6.938 0.592 1.986 8.730
16 7.647 0.592 1.986 8.537
17 7.800 0.592 1.986 8.498
...
...
...
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Received on Mon Oct 18 2010 - 08:30:04 PDT
