the RGBMAX parameter is new to AMBER8. check the manual
for details. AMBER 7 and 8 GB energies can be made to match exactly
by using this parameter.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Fabien Cailliez wrote:
> Dear all,
>
> I wonder if there is a difference in GB calculations between AMBER7
> and AMBER8.
> Indeed I remarked a difference when I calculate the energy of my
> structures when I am running
> MMGBSA calculations. The difference is always around 4 kcal/mol for
> every snapshot for GB energies.
> Here are my results :
> with AMBER 7 :
> # MEAN STD
> # =======================
> ELE -6636.65 68.47
> VDW -700.80 26.89
> INT 4340.43 42.15
> GAS -2997.02 76.28
> GBSUR 61.49 1.23
> GB -3470.58 56.05
> GBSOL -3409.10 55.62
> GBELE -10107.23 27.20
> GBTOT -6406.12 40.64
>
> with AMBER8 :
> # MEAN STD
> # =======================
> ELE -6636.65 68.47
> VDW -700.80 26.89
> INT 4340.43 42.15
> GAS -2997.02 76.28
> PBSUR 61.49 1.23
> PBCAL -3442.74 56.73
> PBSOL -3381.26 56.15
> PBELE -10079.39 36.92
> PBTOT -6378.28 43.33
> GBSUR 61.49 1.23
> GB -3474.91 56.07
> GBSOL -3413.43 55.65
> GBELE -10111.56 27.17
> GBTOT -6410.45 40.63
>
> As can be seen, everything is identical except for GB energies.
> The input scripts for sander which are generated by mm_pbsa.pl are
> the same.
>
> Does anyone have any suggestion ?
>
> Thanks in advance,
> Yours sincerely,
> Fabien
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Jan 18 2005 - 14:53:01 PST
