AMBER Archive (2005)

Subject: Re: AMBER: MM_PBSA problem

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Fri Nov 04 2005 - 12:18:17 CST

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_at_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.outfile 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_at_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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