Can you share with us your mmpba input file and which version of amber you
are using?
Ray
On Sun, Dec 5, 2010 at 7:12 PM, Alice Wang <compu.chem.w.gmail.com> wrote:
> 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 - 22:30:05 PST
