Re: [AMBER] A question regarding mm_pbsa_statistics.pl

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 17 Sep 2010 18:49:38 -0400

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.
>
>
>
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> 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 Fri Sep 17 2010 - 16:00:08 PDT
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