[AMBER] entropy problem

From: Rilei Yu <yulaomao1983.yahoo.com.cn>
Date: Sun, 16 May 2010 09:13:55 +0800 (CST)

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
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