could you please attach the individual values for protein, ligand and
complex ? Where are these high differences coming form ? It is possible that
system is not properly equilibrated and these are some close contacts
between ligand and receptor. Do u have some Ions in the binding interface ?
On Wed, Feb 23, 2011 at 7:47 AM, Nitu Bansal <nitubansal1986.gmail.com>wrote:
> hi all
>
> I am putting up my statistics.out file here. I am not getting rational
> behind the high internal energy and van der Waal energy of the ligands. I
> also extracted frame of the lowest energy after production and generated
> PDB
> using ptraj. No distortion in the ligand was found. When extracted
> snapshots
> of ligand was checked in Sirius Visualizer, it was found distorted.
>
> -----------------------
> # MEAN STD MEAN STD MEAN
> STD
> # ======================= =======================
> =======================
> ELE -15343.40 101.35 -15235.77 101.75 -19.35
> 1.74
> VDW -2121.20 34.56 -2085.09 34.58 957440.23
> 25679.73
> INT 10931.11 61.79 10885.11 61.81 68950.58
> 2022.07
> GAS -6533.49 108.04 -6435.75 108.60 1026371.47
> 25533.50
> PBSUR 126.74 0.99 127.93 0.96 3.62
> 0.02
> PBCAL -5118.17 83.44 -5143.26 83.99 -92.69
> 1.40
> PBSOL -4991.43 83.37 -5015.33 83.92 -89.07
> 1.40
> PBELE -20461.58 40.25 -20379.03 40.15 -112.04
> 1.67
> PBTOT -11524.92 65.33 -11451.08 65.57 1026282.40
> 25533.44
> GBSUR 167.14 1.31 168.73 1.27 3.59
> 0.02
> GB -5192.02 78.25 -5200.97 78.53 -90.67
> 1.52
> GBSOL -5024.88 78.19 -5032.24 78.46 -87.08
> 1.51
> GBELE -20535.42 38.27 -20436.74 38.24 -110.02
> 1.73
> GBTOT -11558.36 62.59 -11467.99 62.77 1026284.39
> 25533.66
>
>
> Please give your suggestions
>
> Thanks in advance.
>
>
>
> --
> Nitu Bansal
> M.S Pharm
> Research Scholar
> Department of Pharmacoinformatics
> S.A.S Nagar NIPER Mohali (Chandigarh)
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>
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Received on Tue Feb 22 2011 - 23:30:03 PST
