Dear Mish,
I attached the prmtop and snapshot file,
Urszula
________________________________________
Von: Sushil Mishra [sushilbioinfo.gmail.com]
Gesendet: Mittwoch, 1. Februar 2012 08:53
An: AMBER Mailing List
Betreff: Re: [AMBER] MMPBSA problem
Can you please forward one snapshot of ligand and LIG.prmtop file only ?
..Mish
On Wed, Feb 1, 2012 at 8:36 AM, Urszula Uciechowska
<urszula.uciechowska.chem.umu.se> wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed Feb 01 2012 - 00:30:03 PST
