AMBER Archive (2008)

Subject: Re: AMBER: internal energy INT is not zero from MM_GBSA

From: sobereva (sobjubao_at_yahoo.com.cn)
Date: Tue Oct 07 2008 - 09:22:57 CDT

Hi,
There may be some potential terms of
bond/angle/dihedral exist between ligand and
receptor.You should check it carefully before you
generate topology file in leap.

Lu Tian

--- flyanping <flyanping_at_hotmail.com> wrote:

>
> Dear Amber community:I used mm_gbsa to calculat
> binding free energies,however the final result
> showed:ELE -8.21 7.60VDW
> -20.20 2.07INT -4.72
> 1.09GAS -33.14 7.93GBSUR
> -3.08 0.16GB 10.08
> 5.45GBSOL 7.00 5.40GBELE
> 1.86 4.77GBTOT -26.14
> 5.06In the tutorial ,it's said the INT = internal
> energy arising from bond, angle and dihedral terms
> in the MM force field. (this term always amounts to
> zero in the single trajectory approach).Mine is not
> 0,what does INT=non zero mean? How it happened
> ?Anything wrong with my calcs?Could any body point
> me out how to modify my simulation to make INT close
> to 0.
> Thanks&regards,Yanping
>
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