Thank you Jason
I checked the *out file, the number is ok
but when I check the mm_pbsa.log, I found the warning, as blew, is it the
reason? how to solve it ? Thanks it again.
=>> Reordering files
Final order:
1. snapshot_com.all.out: -
2. snapshot_rec.all.out: -
3. snapshot_lig.all.out: -
=>> Reading files
Reading snapshot_com.all.out
WARNING: Missing PBCAV for PB in 88 -> Taken from 87
WARNING: Missing PBDIS for PB in 88 -> Taken from 87
WARNING: Missing SURF for MS in 88 -> Taken from 87
Reading snapshot_rec.all.out
Checking consistency of CALC
Checking consistency of DATA
Reading snapshot_lig.all.out
Checking consistency of CALC
Checking consistency of DATA
2010/12/6 Jason Swails <jason.swails.gmail.com>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Dec 05 2010 - 19:30:04 PST
