Hello,
I checked the all.out file, the header includes MM, GB, PB, MS. So do I need to
change these settings? I also checked that link, but still don't know what I
should do.
Thank you very much.
________________________________
From: Alexander Metz <alexander_metz2000.yahoo.de>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wed, September 22, 2010 11:23:07 AM
Subject: Re: [AMBER] A question regarding mm_pbsa_statistics.pl
Hi there,
ELRAELE, EPB, and PBNONPOL are used by a hybrid MM-PB/SA approach, only. So the
statistics script is looking for data that is just not there in the all.out
file. You can work around like here:
http://archive.ambermd.org/200806/0357.html
Also there should be a bugfix and it should be corrected in the newest amber
version. The header in the all.out file should the specify which energy terms
are used for statistics.
I hope this helps,
Alex
++++++++++++++++++++++++++++++++++++++++++++++++++
Alexander Metz (PhD Student)
Heinrich Heine Universität Düsseldorf
Institut für Pharmazeutische und Medizinische Chemie
Computational Pharmaceutical Chemistry
Universitaetsstrasse 1
40225 Düsseldorf, Germany
Tel: +49 211 81 13854
++++++++++++++++++++++++++++++++++++++++++++++++++
________________________________
Von: bin wang <wang_p_z.yahoo.com.cn>
An: AMBER Mailing List <amber.ambermd.org>
Gesendet: Mittwoch, den 22. September 2010, 15:42:16 Uhr
Betreff: Re: [AMBER] A question regarding mm_pbsa_statistics.pl
Thank you for your suggestion. I rerun the mm-pbsa is a new folder but the same
problem happened again. I tried both mm_pbsa.pl and mm_pbsa_statistics.pl, but
neither of them work. When I tried to redo the example from the Amber tutorials
(
http://ambermd.org/tutorials/advanced/tutorial3/section3.htm), the perl scripts
also showed error messages and didn't give me the final output file. I don't
know what the problem is.
________________________________
From: manoj singh <mks.amber.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Mon, September 20, 2010 8:42:23 PM
Subject: Re: [AMBER] A question regarding mm_pbsa_statistics.pl
Most probably, you are getting this error because your data is overwtitten
in the out files. Easiest fix is, delete all .out files, and rerun the
mm_pbsa.in script. And every time you are running mm_pbsa.pl etc, make sure
you are not over writing in existing files.
On Mon, Sep 20, 2010 at 3:37 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Thank you for your suggestion, but when I check the snapshot_com.all.out,
> snapshot_lig.all.out, and
>
> snapshot_rec.all.out, I didn't find any problem. After I run
> binding_energy.mmpbsa, the binding_energy.log showed warnings like these:
>
> =>> Reading files
> Reading snapshot_com.all.out
> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
> WARNING: Missing EPB for PB 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
> WARNING: Missing EPB for PB in 5 -> Taken from 4
> WARNING: Missing PBNONPOL for PB in 6 -> Taken from 5
> WARNING: Missing ELRAELE for PB in 6 -> Taken from 5
> WARNING: Missing EPB for PB in 6 -> Taken from 5
> WARNING: Missing PBNONPOL for PB in 7 -> Taken from 6
> WARNING: Missing ELRAELE for PB in 7 -> Taken from 6
> WARNING: Missing EPB for PB in 7 -> Taken from 6
> WARNING: Missing PBNONPOL for PB in 8 -> Taken from 7
> WARNING: Missing ELRAELE for PB in 8 -> Taken from 7
> WARNING: Missing EPB for PB in 8 -> Taken from 7
> WARNING: Missing PBNONPOL for PB in 9 -> Taken from 8
> WARNING: Missing ELRAELE for PB in 9 -> Taken from 8
> WARNING: Missing EPB for PB in 9 -> Taken from 8
> WARNING: Missing PBNONPOL for PB in 10 -> Taken from 9
> WARNING: Missing ELRAELE for PB in 10 -> Taken from 9
> WARNING: Missing EPB for PB in 10 -> Taken from 9
> WARNING: Missing PBNONPOL for PB in 11 -> Taken from 10
> WARNING: Missing ELRAELE for PB in 11 -> Taken from 10
> WARNING: Missing EPB for PB in 11 -> Taken from 10
> WARNING: Missing PBNONPOL for PB in 12 -> Taken from 11
> WARNING: Missing ELRAELE for PB in 12 -> Taken from 11
> WARNING: Missing EPB for PB in 12 -> Taken from 11
> WARNING: Missing PBNONPOL for PB in 13 -> Taken from 12
> WARNING: Missing ELRAELE for PB in 13 -> Taken from 12
> WARNING: Missing EPB for PB in 13 -> Taken from 12
> WARNING: Missing PBNONPOL for PB in 14 -> Taken from 13
> WARNING: Missing ELRAELE for PB in 14 -> Taken from 13
> WARNING: Missing EPB for PB in 14 -> Taken from 13
> WARNING: Missing PBNONPOL for PB in 15 -> Taken from 14
> WARNING: Missing ELRAELE for PB in 15 -> Taken from 14
> WARNING: Missing EPB for PB in 15 -> Taken from 14
> WARNING: Missing PBNONPOL for PB in 16 -> Taken from 15
> WARNING: Missing ELRAELE for PB in 16 -> Taken from 15
> WARNING: Missing EPB for PB in 16 -> Taken from 15
> ......
>
> I used the binding_energy.mmpbsa in the tutorial, but why it showed these
> warning? And I didn't get the snapshot_statistics.out file.
>
> I am now learning how to use mmpbsa.py, but why the Perl script didn't
> work?
> Could anybody help me? Thank you in advance.
>
>
>
>
>
>
>
>
>
> ________________________________
>
> From: Jason Swails <jason.swails.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Fri, September 17, 2010 6:49:38 PM
> Subject: Re: [AMBER] A question regarding mm_pbsa_statistics.pl
>
> You should take a look at the output files created by mm_pbsa.pl and see
> if
> anything looks unusual, specifically at the 65th snapshot. Another option
> is to try MMPBSA.py found at
> http://ambermd.org/tutorials/advanced/tutorial_3/py_script .
>
> Good luck!
> Jason
>
> On Fri, Sep 17, 2010 at 6:39 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
>
> > Hello everybody,
> > I am trying to use mm_pbsa_statistics.pl to obtain the binding energy of
> > my
> > protein-DNA system. However, I didn't get results and the terminal
> showed
> > warnings like
> >
> > "Missing EPB for PB in 65 -> Taken from 64"
> > "No values for MM_ELE existing -> Skipping"
> > "No values for GB_GBSOL existing -> Skipping"
> > "No values for MM_GAS existing -> Skipping"
> > "=>> Calc delta from raw data
> > No data for 0+0 PB ELRAELE 0"
> >
> > The input file I used is the snapshot_statistics.in generated by
> > extract_coords.mmpbsa. The command I used is:
> > mm_pbsa_statistics.pl 1 1 snapshot_statistics.in snapshot_statistics.out
> >
> > Could anybody tell me how to use the mm_pbsa_statistics.pl? What input
> > file
> > should I use? Thank you very much.
> >
> >
> >
> > _______________________________________________
> > 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
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 27 2010 - 10:30:05 PDT
