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
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Received on Mon Sep 20 2010 - 13:00:03 PDT
