Hi,
Thank you for your kind reply.
I just took the files from the Example file and started running MM-PBSA
method.
I just downloaded required files from Amber-tutorial file and used them for
the analysis.
So, can u suggest among which file the error would be occurred.
with regards,
anogna
On Wed, Dec 5, 2012 at 8:19 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Dec 5, 2012 at 2:23 AM, Anogna <anognal.gmail.com> wrote:
>
> > Dear Amber Users,
> >
> > I have been running some tests with the MM-PBSA suite of perl scripts. I
> > have come across a similar errors as other users faced while doing so.
> >
> > Error i have gone through is:
> >
> > Reading snapshot_com.all.out
> > WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
> > WARNING: Missing PB for PB in 0 -> Taken from -1
> > WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
> > WARNING: Missing PBCAV for PB in 0 -> Taken from -1
> > WARNING: Missing EPB for PB in 0 -> Taken from -1
> > WARNING: Missing PBDIS for PB in 0 -> Taken from -1
> > WARNING: Missing SURF for MS in 0 -> Taken from -1
> > WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0
> > WARNING: Missing ELRAELE for PB in 1 -> Taken from 0
> > WARNING: Missing EPB for PB in 1 -> Taken from 0
> > WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1
> > WARNING: Missing ELRAELE for PB in 2 -> Taken from 1
> > WARNING: Missing EPB for PB in 2 -> Taken from 1
> > WARNING: Missing PBNONPOL for PB in 3 -> Taken from 2
> > WARNING: Missing ELRAELE for PB in 3 -> Taken from 2
> > WARNING: Missing EPB for PB in 3 -> Taken from 2
> > WARNING: Missing PBNONPOL for PB in 4 -> Taken from 3
> > WARNING: Missing ELRAELE for PB in 4 -> Taken from 3
> > WARNING: Missing EPB for PB in 4 -> Taken from 3
> > WARNING: Missing PBNONPOL for PB in 5 -> Taken from 4
> > WARNING: Missing ELRAELE for PB in 5 -> Taken from 4
> >
>
> This means that the PBSA calculations failed. I would suggest looking for
> error messages somewhere in the intermediate output files.
>
>
> > When i Google regarding the error, I found a way to fix the problem from
> > previous mailing list.
> >
>
> The error messages you received don't actually tell you what went wrong.
> The errors you should google are the ones in the intermediate sander
> output files.
>
>
> > As per the suggestions from previous mails,
> >
> > [snip]
> >
>
>
> > patching file src/sander/qm2_load_params_and_allocate.f
> > Reversed (or previously applied) patch detected! Skipping patch.
> > *
> >
> > I do not know how to solve these problems. Can somebody help me with
> this?
> >
>
> This means those bug fixes have already been applied. My suggestion is to
> install AmberTools 12 and try using MMPBSA.py from that package instead.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Wed Dec 05 2012 - 08:00:03 PST
