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,
ligand_mask=':421-432', receptor_mask=':1-210:211-420',
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,
ligand_mask=':421-432', receptor_mask=':1-210:211-420',
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
