thank you for your help! i found that here was error in my delphi.crg file.
now the value of PBCAL is not zero. i have another question need you help.
without calculating the " -TÄS", how to judge the accuracy of result?
On 11/5/05, Scott Pendley <scott.pendley.gmail.com> wrote:
>
> What are you using as your PB solver, Delphi or the amber PB program? If
> you are using Delphi, you may not have it configured correctly so you may
> want to look at that.
>
>
> On 11/4/05, haixiao jin <jinhx952.gmail.com> wrote:
> >
> > dear Olufsen,
> > thank you for your help!
> > in my opinion, the extremely large of INT and GAS is due to six
> > active-site water molecules existence. i didn't find the reason why the
> > value of PBCAL is zero. i run MM_PBSA again by just set the protein as
> > receptor with the active-site water molecules. this time the
> > statistic.out file was get and show below: now the value of INT and GAS
> > become smaller, but the value of PBCAL is still zero.
> >
> > # COMPLEX RECEPTOR LIGAND
> > # ----------------------- -----------------------
> > -----------------------
> > # MEAN STD MEAN STD MEAN STD
> > # ======================= =======================
> > =======================
> > ELE -10256.37 86.13 -9862.92 82.51 -245.73 3.04
> > VDW -1503.97 28.33 -1463.62 28.46 23.52 3.01
> > INT 7265.76 49.13 7158.26 49.98 107.50 5.90
> > GAS -4494.59 94.61 -4168.27 93.55 -114.71 5.34
> > PBSUR 226.57 0.54 224.07 0.56 3.80 0.01
> > PBCAL 0.00 0.00 0.00 0.00 0.00 0.00
> > PBSOL 226.57 0.54 224.07 0.56 3.80 0.01
> > PBELE -10256.37 86.13 -9862.92 82.51 -245.73 3.04
> > PBTOT -4268.01 94.71 -3944.20 93.66 -110.92 5.34
> >
> > # DELTA
> > # -----------------------
> > # MEAN STD
> > # =======================
> > ELE -147.73 13.50
> > VDW -63.88 3.79
> > INT 0.00 0.00
> > GAS -211.60 14.50
> > PBSUR -1.29 0.12
> > PBCAL 0.00 0.00
> > PBSOL -1.29 0.12
> > PBELE -147.73 13.50
> > PBTOT -212.89 14.54
> > and part of my com_all.out file is showed bellow:
> > 1
> > BOND = 1989213.3347 ANGLE = 2846.0146 DIHED = 3371.8589
> > VDWAALS = -2861.7092 EEL = -25222.7929 HBOND = 0.0000
> > 1-4 VDW = 1327.8785 1-4 EEL = 14858.3725 RESTRAINT = 0.0000
> > corrected reaction field energy: 0.0000 kt
> > surface area = 41853.523
> > 2
> > BOND = 1743776.1560 ANGLE = 2888.0949 DIHED = 3331.2946
> > VDWAALS = - 2896.2172 EEL = -25136.0767 HBOND = 0.0000
> > 1-4 VDW = 1343.4143 1-4 EEL = 14936.0625 RESTRAINT = 0.0000
> > corrected reaction field energy: 0.0000 kt
> >
> > On 11/4/05, Magne Olufsen <Magne.Olufsen.chem.uit.no > wrote:
> > >
> > >
> > > Hii
> > > Your INT energy is extremly large. Try to load your simulated
> > > structure into a graphical program (O, pymol etc) to see if you have any
> > > close contacts or bonds that should'nt be there. You also might try a
> > > minimization with sander, the output tells you the atom with the highest
> > > energy gradient. this might help you locate the if there are a strange bond
> > > etc.
> > >
> > > If you are using DelPhi to calculate PB, you should check your delphi
> > > out file to see if you get any error message.
> > >
> > > I hope this will help,
> > >
> > >
> > >
> > > Greetings from Magne Olufsen
> > >
> > >
> > > At 07:43 04.11.2005, you wrote:
> > >
> > > dear amber users,
> > > The MM_PBSA was performed without any error emerged. But the value of
> > > PBCAL (reaction field energy calculated by PB) in the statistics.outfile is zero. Why did it happen? The only special in my system is that six
> > > active-site water molecules were considered as recepter with the protein.
> > > Here is the statistic.out file:
> > >
> > > # COMPLEX RECEPTOR LIGAND
> > > # ----------------------- -----------------------
> > > -----------------------
> > > # MEAN STD MEAN STD MEAN STD
> > > # ======================= =======================
> > > =======================
> > > ELE -10282.99 84.37 -9891.06 79.67 -245.73 3.04
> > > VDW -1503.96 28.45 -1463.47 28.60 23.52 3.01
> > > INT 2453220.43 665175.31 2453112.93 665174.64 107.50 5.90
> > > GAS 2441433.48 665174.79 2441758.41 665167.82 -114.71 5.34
> > > PBSUR 227.76 0.54 225.25 0.55 3.80 0.01
> > > PBCAL 0.00 0.00 0.00 0.00 0.00 0.00
> > > PBSOL 227.76 0.54 225.25 0.55 3.80 0.01
> > > PBELE -10282.99 84.37 -9891.06 79.67 -245.73 3.04
> > > PBTOT 2441661.24 665174.65 2441983.65 665167.66 -110.92 5.34
> > >
> > > # DELTA
> > > # -----------------------
> > > # MEAN STD
> > > # =======================
> > > ELE -146.20 12.60
> > > VDW -64.01 3.79
> > > INT -0.00 0.00
> > > GAS -210.21 13.37
> > > PBSUR -1.29 0.12
> > > PBCAL 0.00 0.00
> > > PBSOL -1.29 0.12
> > > PBELE -146.20 12.60
> > > PBTOT -211.50 13.40
> > >
> > > any advise will be appreciated. thank you!
> > >
> > >
> > >
> > >
> > >
> >
>
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Received on Mon Nov 07 2005 - 09:53:01 PST
