AMBER Archive (2008)

Subject: Re: AMBER: MM_PBSA output file

From: Navnit Kumar Mishra (navnit_at_chemi.muni.cz)
Date: Fri May 09 2008 - 11:21:17 CDT

Qi Yan wrote:

> Hi,all:
>
> I got the mm_pbsa output file of first frame of complex as below.
>
> 1
> BOND = 1600.1333 ANGLE = 4318.0104 DIHED =
> 5111.4772
> VDWAALS = -3906.3871 EEL = -17702.1364 HBOND =
> 0.0000
> 1-4 VDW = 1942.8613 1-4 EEL = 12718.1410 RESTRAINT =
> 0.0000
> corrected reaction field energy: -5427.619771
> surface area = 31174.361
> ECAVITY = 31174.361
> EDISPER = 0.0000
>
> I know the ELE = EEL + 1-4EEL;
> VDW = VDWAALS + 1-4 VDW;
> PBSUR = surface area * SURFTEN + SURFOFF.
>
> However, I have no idea PBCAL = ? Does anybody point me out?
>

The corrected reaction field energy is reported by the mmpbsa script is
in KT, so you need to convert it into kcal/mol. It is done in this way.
PBCAL= (Corrected reaction field energy) x (((R (8.314) x TEMP(298K)) /
4.184)/1000.0)

.. navnit....

>
> Thanks in advance,
>
> Qi
>

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