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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Received on Wed Dec 05 2012 - 07:00:02 PST
