AMBER Archive (2006)

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

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Thu Jun 29 2006 - 18:56:34 CDT

It's from AMBER8, thanks!

On Thu, 29 Jun 2006 21:47:13 -0300, Ray Luo <rluo_at_uci.edu> wrote:

> Is this from Amber8 or Amber9?
>
> Best,
> Ray
>
> yxiong99 wrote:
>
>> 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 <mailto:yxiong99_at_163.com>
>> 　　　　　　　　　　2006-06-29
>>
>>
>>
>>
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