AMBER Archive (2006)

Subject: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl

From: yxiong99 (yxiong99_at_163.com)
Date: Thu Jun 29 2006 - 15:49:50 CDT

Dear sir,
   I made a test on one snapshot of MD to do MM_PBSA. The first, I directly calculate the binding enery with the command:
mm_pbsa.pl *.in *.out, and the results are (1)
    The second, I use the calculated output (complex.out, receptor.out,ligand.out) which were gotten from the first calculation to recalculate binding energy with the command: mm_pbsa_statistics.pl 1 0 *.in *.out The results are (2).
   I am so surprised that the result(1) and (2) are different because in fact mm_pbsa.pl should also use the command mm_pbsa_statistics.pl when it calculated binding energy.
   I notice the difference come from the calculation for PBSUR.
As for the results (1), their PBSUR are the values of "surfact area" multiplied by 0.005. However as for the results (2), their PBSUR are the values of "surfact area" multiplied by 0.00544465,0.005444388,0.006804612 for complex,receptor and ligand respectively. I am confused with these different coefficient.
    I will be appreciated if anyone can help me understand their two commands.
complex.out
----------------------------------------------
1
 BOND = 956.9142 ANGLE = 3438.7808 DIHED = 4881.3984
 VDWAALS = -5728.5812 EEL = -43793.2330 HBOND = 0.0000
 1-4 VDW = 2445.3638 1-4 EEL = 23378.8962 RESTRAINT = 0.0000
corrected reaction field energy: -28857.870000
surface area = 37447.769
------------------------------------------------
receptor.out
------------------------------------------------
    BOND = 948.5462 ANGLE = 3393.9359 DIHED = 4876.3363
 VDWAALS = -5652.4080 EEL = -43315.2732 HBOND = 0.0000
 1-4 VDW = 2425.9662 1-4 EEL = 23183.8960 RESTRAINT = 0.0000
corrected reaction field energy: -29417.050000
surface area = 37726.925
------------------------------------------------
ligand.out
------------------------------------------------
 BOND = 8.3680 ANGLE = 44.8449 DIHED = 5.0621
 VDWAALS = -3.9334 EEL = -106.8249 HBOND = 0.0000
 1-4 VDW = 19.3976 1-4 EEL = 195.0002 RESTRAINT = 0.0000
corrected reaction field energy: -162.375800
surface area = 665.725
------------------------------------------------

The result(1)
-----------------------------------------------------------------------------------
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -20414.34 0.00 -20131.38 0.00 88.18 0.00
VDW -3283.22 0.00 -3226.44 0.00 15.46 0.00
INT 9277.09 0.00 9218.82 0.00 58.28 0.00
GAS -14420.46 0.00 -14139.00 0.00 161.91 0.00
PBSUR 187.24 0.00 188.63 0.00 3.33 0.00
PBCAL -17202.99 0.00 -17536.33 0.00 -96.80 0.00
PBSOL -17015.75 0.00 -17347.70 0.00 -93.47 0.00
PBELE -37617.32 0.00 -37667.71 0.00 -8.62 0.00
PBTOT -31436.21 0.00 -31486.70 0.00 68.45 0.00
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -371.13 0.00
VDW -72.24 0.00
INT -0.00 0.00
GAS -443.37 0.00
PBSUR -4.72 0.00
PBCAL 430.14 0.00
PBSOL 425.42 0.00
PBELE 59.00 0.00
PBTOT -17.96 0.00
---------------------------------------------------------------------------------------
The result (2)
---------------------------------------------------------------------------------------
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -20414.34 0.00 -20131.38 0.00 88.18 0.00
VDW -3283.22 0.00 -3226.44 0.00 15.46 0.00
INT 9277.09 0.00 9218.82 0.00 58.28 0.00
GAS -14420.46 0.00 -14139.00 0.00 161.91 0.00
PBSUR 203.89 0.00 205.40 0.00 4.53 0.00
PBCAL -17202.99 0.00 -17536.33 0.00 -96.80 0.00
PBSOL -16999.10 0.00 -17330.93 0.00 -92.27 0.00
PBELE -37617.32 0.00 -37667.71 0.00 -8.62 0.00
PBTOT -31419.56 0.00 -31469.93 0.00 69.65 0.00
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -371.13 0.00
VDW -72.24 0.00
INT -0.00 0.00
GAS -443.37 0.00
PBSUR -6.04 0.00
PBCAL 430.14 0.00
PBSOL 424.10 0.00
PBELE 59.00 0.00
PBTOT -19.28 0.00
---------------------------------------------------------------------------------------
　　　　　　　　Ying Xiong
　　　　　　　　yxiong99_at_163.com
　　　　　　　　　　2006-06-29
 
 
 
 
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