Dear amber users,
Last time, I ever asked the same problem: when I tried to calculate the entropy contribution to my system, I found it failed for the receptor part. Last time I used homology model, but this time, I changed to the crystal structure. However, this problem was still not solved. Can anyone give me more suggestions? Or can I send my system to you, in order to find the problem easier?
Sun May 16 00:12:49 EST 2010
Input file:
--------------------------------------------------------------
MMPBSA input file to run gb
&general
startframe=250, endframe=250, interval=1, verbose=0,
ligand_mask=':411-427', receptor_mask=':1-205:206-410',
initial_traj=0,
/
&nmode
nmstartframe=1, nmendframe=1,
nminterval=1,
/
end
--------------------------------------------------------------
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 1 frames.
NMODE calculations performed using 1 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: 14.4288 0.0000
Rotational: 13.0056 0.0000
Vibrational: 154.7418 0.0000
Total: 182.1762 0.0000
DELTA S total= -1.0000 +/- 0.0000
NOTE: All entropy results have units kcal/mol. (Temperature has already been multiplied in as 300. K)
-------------------------------------------------------------------------------
Very thanks!
Rilei Yu
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Received on Sat May 15 2010 - 18:30:04 PDT
