Yes I have checked that, and they looked correct ...
/Urszula
________________________________________
Von: mish [smncbr.gmail.com]
Gesendet: Mittwoch, 1. Februar 2012 07:41
An: AMBER Mailing List
Betreff: Re: [AMBER] MMPBSA problem
Hello,
It sound like that there are some vdW clashes in the snapshots. Do you see
the correct structure of complex, protein and ligand when you load their
snapshots with COM.prmtop, REC,prmtop and LIG.prmtop * from same directory)
in vmd ?. If you have not tried it, just check the structures properly so
that one can be sure that snapshots generated here are correct for
the particular topology file.
..Mish
On Wed, Feb 1, 2012 at 7:26 AM, Urszula Uciechowska <
urszula.uciechowska.chem.umu.se> wrote:
> Dear Amber users,
>
> I am running MMPBSA calcuations for 100sps, my input file for that is:
>
> #
> # Input parameters for mm_pbsa.pl
> #
> #
>
> ################################################################################
> #
> VERBOSE 0
> PARALLEL 0
> #
> PREFIX L
> PATH ./
> START 1
> STOP 1
> 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
> #
>
> ################################################################################
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> INP 1
> #
> SURFTEN 0.04356
> SURFOFF -1.008
> #
> IVCAP 0
> CUTCAP -1.0
> XCAP 0.0
> YCAP 0.0
> ZCAP 0.0
> #
>
> ################################################################################
> .MM
> #
> # MM parameters (this section is only relevant if MM = 1 above)
> #
> # The following parameters are passed to sander.
> # For further details see the sander documentation.
> #
> # DIELC - Dielectricity constant for electrostatic interactions.
> # Note: This is not related to GB calculations.
> #
> DIELC 1.0
> #
>
> ################################################################################
> # the desolvation according to Gnp = SURFTEN * SASA +
> SURFOFF.
> #
> IGB 5
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
>
> ################################################################################
> .MS
> #
> # Molsurf parameters (this section is only relevant if MS = 1 above)
> #
> # PROBE - Radius of the probe sphere used to calculate the SAS.
> # In general, since Bondi radii are already augmented by 1.4A,
> # PROBE should be 0.0
> # In IVCAP = 1 or 5, the solvent excluded surface is required for
> # calculating the cavity contribution. Bondi radii are not
> # augmented in this case and PROBE should be 1.4.
> #
> PROBE 0.0
> #
>
> ################################################################################
>
> but the energy that I am getting is huge ...
>
>
>
>
> # COMPLEX RECEPTOR LIGAND
> # ----------------------- -----------------------
> -----------------------
> # MEAN STD MEAN STD MEAN
> STD
> # ======================= =======================
> =======================
> ELE -10841.03 101.25 -10410.47 96.18 -190.08
> 17.55
> VDW -1543.33 28.21 -1466.58 27.14 195120.40
> 4894.33
> INT 8334.19 51.25 8119.96 49.62 168750.44
> 12093.84
> GAS -4050.18 109.39 -3757.09 105.02 363680.75
> 13158.43
> PBSUR 927.79 6.78 927.94 6.33 77.73
> 1.32
> PBCAL -6405.31 89.46 -6405.69 83.25 -437.07
> 13.88
> PBSOL -5477.52 87.33 -5477.76 80.88 -359.33
> 14.13
> PBELE -17246.34 36.97 -16816.16 36.62 -627.15
> 9.25
> PBTOT -9527.70 53.87 -9234.85 52.03 363321.42
> 13157.67
> GBSUR 153.52 1.12 153.54 1.05 13.02
> 0.22
> GB -3611.13 96.16 -3775.40 90.77 -310.76
> 13.24
> GBSOL -3457.61 95.80 -3621.85 90.41 -297.75
> 13.26
> GBELE -14452.16 62.85 -14185.86 58.91 -500.85
> 11.48
> GBTOT -7507.79 78.59 -7378.94 75.06 363383.00
> 13157.15
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -240.48 140.75
> VDW -195197.15 4894.48
> INT -168536.20 12094.05
> GAS -363973.84 13159.30
> PBSUR -77.88 9.37
> PBCAL 437.45 122.98
> PBSOL 359.57 119.87
> PBELE 196.97 52.85
> PBTOT -363614.26 13157.88
> GBSUR -13.04 1.55
> GB 475.03 132.90
> GBSOL 461.99 132.39
> GBELE 234.55 86.90
> GBTOT -363511.84 13157.60
>
>
> when I am running MMPBSA.py for the same snapshots the energies are :
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -86.1604 4.7220
> 0.4722
> EEL -322.6536 22.3014
> 2.2301
> EGB 357.6727 20.9844
> 2.0984
> ESURF -12.0810 0.4190
> 0.0419
>
> DELTA G gas -408.8140 20.9551
> 2.0955
> DELTA G solv 345.5916 20.9989
> 2.0999
>
>
> DELTA G binding = -63.2223 +/- 3.8132
> 0.3813
>
>
> What is the problem here? For MMPBSA.py I am not able to get PB energy,
> with GB there is no problem...
> Thank you in advance for any suggestions,
>
> /Urszula
>
>
>
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Received on Wed Feb 01 2012 - 00:00:03 PST
