AMBER Archive (2008)

Subject: Re: AMBER: MM_PBSA output file

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Fri May 09 2008 - 11:22:35 CDT

"ELE = electrostatic energy as calculated by the MM force field.
VDW = van der Waals contribution from MM.
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).
GAS = total gas phase energy (sum of ELE, VDW and INT).
PBSUR/GBSUR = nonpolar contribution to the solvation free energy
calculated by an empirical model.
PBCAL/GB = the electrostatic contribution to the solvation free energy
calculated by PB or GB respectively.
PBSOL/GBSOL = sum of nonpolar and polar contributions to solvation.
PBELE/GBELE = sum of the electrostatic solvation free energy and MM
electrostatic energy.
PBTOT/GBTOT = final estimated binding free energy calculated from the
terms above. (KCal/mol)"

From

http://amber.scripps.edu/tutorials/advanced/tutorial3/section3.htm

Hope this helps,

--alessandro

On Fri, May 9, 2008 at 9:03 AM, Qi Yan <kid1412_at_uab.edu> 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?
>
> Thanks in advance,
>
> Qi
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