Dear Son Tung,
Thanks for your reply, yeah, I know that I didn't calculate entropy.
However, I still don't understand the reason for the big difference between
them, since I used the same trajectory. Thanks.
Best Regards,
Qinghua
On Sat, Dec 17, 2011 at 12:09 AM, Ngo Son Tung <nstung.ifpan.edu.pl> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Ngo Son Tung
>
>
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Received on Sat Dec 17 2011 - 15:00:03 PST
