After waiting for three days, the entropy calculation for one frame of my system was finished! Unfortunately, all results showed to me is NO NMODE ENTROPY CALCULATED. SNAPSHOTS NOT MINIMIZED!
It looks like my system is so special that entropy calculation cannot be performed. Is this time still the converge problem using updated script? To this point, I am a bit of disappointed!
The results as follows:
| Run on Sat Jun 5 04:42:48 EST 2010
|Input file:
|--------------------------------------------------------------
|MMPBSA everything
|&general
| startframe=1, endframe=1,
| entropy=0, keep_files=0,
|/
|&gb
| igb=5, saltcon=0.15,
|/
|&pb
| istrng=0.15,
|# sander_apbs=1,
|/
|&nmode
| maxcyc=50000, ala_entropy=0, nmode_istrng=0.15,
|/
|
|
|
|
|--------------------------------------------------------------
|Complex topology file: complex.prmtop
|Receptor topology file: re.prmtop
|Ligand topology file: lig.prmtop
|Initial mdcrd(s): complex_md0.mdcrd
|
|Best guess for receptor mask: ":1-420"
|Best guess for ligand mask: ":421-432"
|Calculations performed using 1 frames.
|NMODE calculations performed using 1 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
|All entropy results have units kcal/mole (Temperature is 298.15 K).
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
NO NMODE ENTROPY CALCULATED. SNAPSHOTS NOT MINIMIZED!
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -3836.8981 0.0000 0.0000
EEL -29831.2025 0.0000 0.0000
EGB -4275.4807 0.0000 0.0000
ESURF 142.3725 0.0000 0.0000
G gas -33668.1006 0.0000 0.0000
G solv -4133.1082 0.0000 0.0000
TOTAL -37801.2088 0.0000 0.0000
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -3702.0048 0.0000 0.0000
EEL -28994.9903 0.0000 0.0000
EGB -4145.3888 0.0000 0.0000
ESURF 144.4286 0.0000 0.0000
G gas -32696.9951 0.0000 0.0000
G solv -4000.9602 0.0000 0.0000
TOTAL -36697.9553 0.0000 0.0000
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -48.8611 0.0000 0.0000
EEL -783.3506 0.0000 0.0000
EGB -217.3343 0.0000 0.0000
ESURF 9.1300 0.0000 0.0000
G gas -832.2117 0.0000 0.0000
G solv -208.2043 0.0000 0.0000
TOTAL -1040.4160 0.0000 0.0000
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -86.0322 0.0000 0.0000
EEL -52.8616 0.0000 0.0000
EGB 87.2424 0.0000 0.0000
ESURF -11.1861 0.0000 0.0000
DELTA G gas -138.8938 0.0000 0.0000
DELTA G solv 76.0563 0.0000 0.0000
DELTA G binding = -62.8375 +/- 0.0000 0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using Normal Mode Entropy Approximation: DELTA G binding = -62.8375 +/- 0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -3836.8981 0.0000 0.0000
EEL -29831.2025 0.0000 0.0000
EPB -4242.3267 0.0000 0.0000
ECAVITY 106.2150 0.0000 0.0000
G gas -33668.1006 0.0000 0.0000
G solv -4136.1117 0.0000 0.0000
TOTAL -37804.2123 0.0000 0.0000
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -3702.0048 0.0000 0.0000
EEL -28994.9903 0.0000 0.0000
EPB -4112.4700 0.0000 0.0000
ECAVITY 107.7342 0.0000 0.0000
G gas -32696.9951 0.0000 0.0000
G solv -4004.7358 0.0000 0.0000
TOTAL -36701.7309 0.0000 0.0000
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -48.8611 0.0000 0.0000
EEL -783.3506 0.0000 0.0000
EPB -220.4057 0.0000 0.0000
ECAVITY 5.8770 0.0000 0.0000
G gas -832.2117 0.0000 0.0000
G solv -214.5287 0.0000 0.0000
TOTAL -1046.7404 0.0000 0.0000
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -86.0322 0.0000 0.0000
EEL -52.8616 0.0000 0.0000
EPB 90.5490 0.0000 0.0000
ECAVITY -7.3962 0.0000 0.0000
DELTA G gas -138.8938 0.0000 0.0000
DELTA G solv 83.1528 0.0000 0.0000
DELTA G binding = -55.7410 +/- 0.0000 0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using Normal Mode Entropy Approximation: DELTA G binding = -55.7410 +/- 0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
I have to admit that it works well for little system.BUt it is not the same story for my system. Here, I am sorry for my complain.
Best wishes,
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 04 2010 - 18:30:03 PDT
