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.out file
> 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 Fri Nov 04 2005 - 09:53:00 PST
