Dear Qinghua,
I thinks you don't calculate entropy distribution.
Regards,
Son Tung.
> Dear Amber users,
>
> Here are the results of the binding energy calculated by python and perl
> mm/pbsa respectively, and also the input files are showed here.
>
> the input file for calculation of perl version:
>
> .GENERAL
> VERBOSE 0
> PARALLEL 8
> #
> PREFIX snapshot
> PATH ../snapshots/
> START 1
> STOP 400
> OFFSET 1
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ../com.prmtop
> RECPT ../rec.prmtop
> LIGPT ../lig.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 1
> #
> NM 0
> #
> ################################################################################
> .PB
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.10
> RADIOPT 1
> INP 1
> #
> SURFTEN 0.00542
> SURFOFF -1.008
> #
> IVCAP 0
> CUTCAP -1.0
> XCAP 0.0
> YCAP 0.0
> ZCAP 0.0
> #
> ################################################################################
> .MM
> #
> DIELC 1.0
> #
> ################################################################################
> .GB
> #
> IGB 5
> GBSA 2
> SALTCON 0.10
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> ################################################################################
> .MS
> PROBE 0.0
> ################################################################################
> .PROGRAMS
> # Additional program executables can be defined here
> ################################################################################
>
> and here are the results:
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -269.04 11.21
> VDW -63.58 4.63
> INT -0.00 0.01
> GAS -332.63 10.49
> PBSUR -6.10 0.26
> PBCAL 290.70 9.67
> PBSOL 284.60 9.64
> PBELE 21.66 6.73
> PBTOT -48.03 5.32
> GBSUR -9.44 0.34
> GB 204.37 23.16
> GBSOL 194.93 23.20
> GBELE -64.67 22.01
> GBTOT -137.70 22.03
>
> For the python case, the input file is:
>
> &general
> startframe=1, endframe=400, interval=1,
> verbose=1, keep_files=1,
> /
> &gb
> igb=5, saltcon=0.10, surften=0.0072, surfoff=0.00,
> /
> &pb
> indi=1.0, exdi=80.0, scale=2.0, linit=1000, prbrad=1.4,
> inp=1, istrng=0.10, cavity_surften=0.00542, cavity_offset=-1.008,
> fillratio=4.0,
> /
>
> and the results of the calculation are:
>
> GB:
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> VDWAALS -63.5848 4.6231
> 0.2312
> EEL -269.0419 11.1926
> 0.5596
> EGB 259.9393 9.7870
> 0.4893
> ESURF -8.0095 0.3432
> 0.0172
>
> DELTA G gas -332.6283 10.4807
> 0.5240
> DELTA G solv 251.9298 9.8082
> 0.4904
>
> DELTA G binding = -80.6986 +/- 5.1168
> 0.2558
>
> PB:
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> VDWAALS -63.5848 4.6231
> 0.2312
> EEL -269.0419 11.1926
> 0.5596
> EPB 284.6789 8.9675
> 0.4484
> ECAVITY -6.2191 0.2638
> 0.0132
>
> DELTA G gas -332.6283 10.4807
> 0.5240
> DELTA G solv 278.4598 8.9624
> 0.4481
>
> DELTA G binding = -54.1686 +/- 4.8905
> 0.2445
>
> By comparision, we can see that there is a big difference, which is mainly
> generated by the solvation free energy. The same situation also exists in
> another case. From the input files, I tried to choose the same parameters,
> but... So how should I treat the two different results, or how should I
> reset the parameters? Thanks very much!
>
> --
> Best Regards,
>
> Qinghua
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>
--
Ngo Son Tung
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Received on Fri Dec 16 2011 - 15:30:03 PST
