AMBER Archive (2006)

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

From: Ray Luo (rluo_at_uci.edu)
Date: Thu Jun 29 2006 - 19:47:13 CDT

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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-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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