Look at the temporary output files created by sander and see if the numbers
make sense. Depending on the version of mm_pbsa that you're using, either
pbsa_com.#.out, pbsa_rec.#.out, pbsa_lig.#.out (for amber10/amber11, I
think) and sander_com.#.out, etc.
Make sure you set VERBOSE to a proper setting so that it keeps all of the
files. See the amber manual for a more detailed discussion.
All the best,
Jason
On Sun, Dec 5, 2010 at 9:26 PM, Alice Wang <compu.chem.w.gmail.com> wrote:
> Dear Amber,
>
> My pbsa out put file is blow:
> # COMPLEX RECEPTOR
> LIGAND
> # ----------------------- -----------------------
> -----------------------
> # MEAN STD MEAN STD
> MEAN STD
> # ======================= =======================
> =======================
> ELE -6803.94 114.19 -6670.34 114.97
> -101.61 1.59
> VDW -1772.99 26.24 -1734.65 26.33
> 5.04 1.38
> INT 16439.74 2118.23 16405.28 2118.61
> 34.47 3.69
> GAS 7862.82 2103.51 8000.29 2101.62
> -62.10 3.76
> PBSUR 157.30 1.27 158.36 1.29
> 3.21 0.02
> PBCAL -8491.30 115.80 -8517.82 116.78
> -20.24 1.30
> PBSOL -8333.99 115.33 -8359.46 116.33
> -17.03 1.30
> PBELE -15295.23 43.75 -15188.16 43.63
> -121.85 1.32
> PBTOT -471.17 2106.88 -359.17 2106.46
> -79.13 3.67
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -31.99 3.11
> VDW -43.38 2.20
> INT -0.00 0.00
> GAS -75.37 3.88
> PBSUR -4.26 0.21
> PBCAL 46.76 3.32
> PBSOL 42.50 3.36
> PBELE 14.77 2.58
> PBTOT -32.87 3.02
>
> The STD value is high in the PBTOT of complex, receptor.
>
> Is it wrong?
>
> Thanks !
>
> Alice Wang
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Dec 05 2010 - 19:00:02 PST
