AMBER Archive (2008)

Subject: Re:Re: AMBER: about mmpbsa out data

From: ecustipp (ecustipp_at_163.com)
Date: Wed Dec 24 2008 - 03:11:50 CST


Thank Dr. Thomas Steinbrecher very much!
I'd check disulphide bridge, it's ok.
My protein is homology model. Does it means that the model is improper or the binding model is improper?
I had 2 MD runs. The other one is the same protein with different binding mode(also one residue's sidechian conformation is different).
The other MD rus's pbsa result is:
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -11291.76 122.30 -11218.50 122.59 -57.93 2.47
VDW -2444.51 35.72 -2396.07 35.40 1.68 2.49
INT 12107.08 78.95 11980.73 76.88 126.34 6.52
GAS -1629.19 152.13 -1633.83 151.01 70.09 6.92
PBSUR 176.72 2.04 177.60 2.23 6.39 0.10
PBCAL -7323.05 105.40 -7336.85 105.60 -34.44 1.76
PBSOL -7146.33 105.45 -7159.24 105.68 -28.05 1.73
PBELE -18614.81 49.49 -18555.35 48.77 -92.38 1.48
PBTOT -8775.52 93.34 -8793.08 90.33 42.04 6.50

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -15.32 7.19
VDW -50.12 3.15
INT -0.00 0.00
GAS -65.44 8.25
PBSUR -7.28 0.37
PBCAL 48.24 9.07
PBSOL 40.96 9.12
PBELE 32.92 6.17
PBTOT -24.48 5.80

This MD run sames more normal.
So, with more information, is it ok for my pbsa analysis for my first MD runs?
Thanks Very Much!
 
 

2008-12-24steinbrt_at_rci.rutgers.edu д
>Hi, Alice,
>
>> the PBTOT for "Complex", "Receptor", "ligand" seems abnormal: Large STD
>> and positive PBTOT for receptor and ligand.
>> So, I'm wander is this out data believable?
>> Thanks in advance!!!
>
>What you see is not bad per se. The absolute energy of a molecule as
>calculated by a forcefield is not a meaningful quantity in itself. You
>need to construct a thermodynamic cycle in which all the non-physical
>terms cancel out, and taking the difference between the COM and LIG+REC
>values in MM-PBSA is one way to do that.
>
>Note that the PBCAL part of both the receptor and complex are fairly
>negative, as they should be, since PBCAL should give you the (in principle
>physically meaningful if hardly measureable) absolute solvation free
>energy of the molecule.
>
>In contrast, the internal energy of the protein is given by the forcefield
>terms which are only designed to give relative conformational energies,
>not absolute ones.
>
>The large stddev for the INT terms is more of a concern and it is
>cancelling out suspiciously well in the final difference. Without more
>knowledge of your system its hard to judge whats going on.
>
>Just one guess: Is it possible that your simulation had a disulphide
>bridge that you forgot to put into the waterless prmtops for MM-PBSA? This
>would explain the large fluctuations but cancel in your end result.
>
>Note that you get a fairly reasonyble total deltaG of -16 kcal, so maybe
>your doing fine...
>
>Regards and Happy Holidays,
>
>Dr. Thomas Steinbrecher
>BioMaps Institute
>Rutgers University
>610 Taylor Rd.
>Piscataway, NJ 08854
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