# [AMBER] Entropy-problem

From: Rilei Yu <yulaomao1983.yahoo.com.cn>
Date: Thu, 15 Apr 2010 06:11:36 +0800 (CST)

Dear amber users,

I spend very long time to finish the entropy calculation for a series of compex, what really makes me feel unexpected is the final values are completely the same (DELTA S total=        -1.0000 +/-       0.0000). Can anyone give me some help? I am really appreciated!

The following are two examples:
Wed Apr 14 22:02:54 EST 2010

Input file:
--------------------------------------------------------------
MMPBSA input file to run gb
&general
startframe=200, endframe=450, interval=50, verbose=0,
initial_traj=0,
&nmode
nmstartframe=1, nmendframe=6,
nminterval=1,
/
--------------------------------------------------------------
Solvated complex topology file:  complex_solvated.prmtop
Complex topology file:           complex.prmtop
Receptor topology file:          re.prmtop
Ligand topology file:            lig.prmtop
Initial mdcrd:                   complex_md2.mdcrd

Calculations performed using 6 frames.
NMODE calculations performed using 6 frames.

All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:

Complex:
Entropy Term          Average        Std. Dev.
-----------------------------------------------------------
Translational:        -1.0000           0.0000
Rotational:           -1.0000           0.0000
Vibrational:          -1.0000           0.0000
Total:                -1.0000           0.0000

Receptor:
Entropy Term          Average        Std. Dev.
-----------------------------------------------------------
Translational:        -1.0000           0.0000
Rotational:           -1.0000           0.0000
Vibrational:          -1.0000           0.0000
Total:                -1.0000           0.0000

Ligand:
Entropy Term          Average        Std. Dev.
-----------------------------------------------------------
Translational:        14.2461           0.0000
Rotational:           12.7523           0.0048
Vibrational:         124.0036           1.2164
Total:               151.0020           1.2147

DELTA S total=        -1.0000 +/-       0.0000

NOTE: All entropy results have units kcal/mol. (Temperature has already been multiplied in as 300. K)
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Wed Apr 14 23:24:22 EST 2010

Input file:
--------------------------------------------------------------
MMPBSA input file to run gb
&general
startframe=200, endframe=450, interval=50, verbose=0,
initial_traj=0,
&nmode
nmstartframe=1, nmendframe=6,
nminterval=1,
/
--------------------------------------------------------------
Solvated complex topology file:  complex_solvated.prmtop
Complex topology file:           complex.prmtop
Receptor topology file:          re.prmtop
Ligand topology file:            lig.prmtop
Initial mdcrd:                   complex_md2.mdcrd

Calculations performed using 6 frames.
NMODE calculations performed using 6 frames.

All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:

Complex:
Entropy Term          Average        Std. Dev.
-----------------------------------------------------------
Translational:        -1.0000           0.0000
Rotational:           -1.0000           0.0000
Vibrational:          -1.0000           0.0000
Total:                -1.0000           0.0000

Receptor:
Entropy Term          Average        Std. Dev.
-----------------------------------------------------------
Translational:        -1.0000           0.0000
Rotational:           -1.0000           0.0000
Vibrational:          -1.0000           0.0000
Total:                -1.0000           0.0000

Ligand:
Entropy Term          Average        Std. Dev.
-----------------------------------------------------------
Translational:        14.1768           0.0000
Rotational:           12.6221           0.0011
Vibrational:         113.2362           0.4890
Total:               140.0351           0.4903

DELTA S total=        -1.0000 +/-       0.0000

NOTE: All entropy results have units kcal/mol. (Temperature has already been multiplied in as 300. K)
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Rilei Yu
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Received on Wed Apr 14 2010 - 15:30:02 PDT
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