I checked the backbone rmsd and protein is euillibirated.
and there are no ions in the binding area.
On Wed, Feb 23, 2011 at 12:31 PM, Sushil Mishra <sushilbioinfo.gmail.com>wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Nitu Bansal
M.S Pharm
Research Scholar
Department of Pharmacoinformatics
S.A.S Nagar NIPER Mohali (Chandigarh)
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Received on Thu Feb 24 2011 - 04:30:07 PST
