AMBER Archive (2005)

Subject: Re: AMBER: MM_PBSA problem

From: Magne Olufsen (Magne.Olufsen_at_chem.uit.no)
Date: Fri Nov 04 2005 - 01:50:30 CST

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!
>
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu