Dear Bill
Thanks for your useful recommendation.
Cheers,
Maryam
--- On Sun, 19/12/10, Bill Miller III <brmilleriii.gmail.com> wrote:
From: Bill Miller III <brmilleriii.gmail.com>
Subject: Re: [AMBER] problem with MM-PBSA
To: "AMBER Mailing List" <amber.ambermd.org>
Received: Sunday, 19 December, 2010, 4:16 PM
This is a fairly well-documented issue in the archives. You will need to
edit the $AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm file. Find where the
PB input file is written within that file (searching for &pb in
mm_pbsa_createinput.pm), and add a line for fillratio in the PB input file;
most often fillratio is increased to 4 (i.e. fillratio=4) when this error
occurs. You will also need to re-compile mm_pbsa.pl after doing a `make
clean`.
Alternatively, the MMPBSA.py python script (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/) allows the user
to change fillratio in the input file, and actually has fillratio set to 4
by default to avoid this error.
Good luck!
-Bill
On Sun, Dec 19, 2010 at 6:06 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com>wrote:
> Dear All
>
> I am trying to calculate the binding energy of ligand-receptor complex and
> I mutated one of the residues to ALA, after extracting the coordinates of
> ligand, receptor and complex, I tried to run the $AMBERHOME/exe/mm_pbsa.plbinding_energy.mmpbsa > binding_energy.log, after that the program stopped
> suddenly while it was calculating the energy of ligand. I checked everything
> related to files.
>
> Here is the file of pbsa_lig.1.out:
>
> .
> .
> .
>
> -------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
> NB-update: residue-based nb list 3771
> NB-update: atom-based nb list 2847
>
> ======== Setting up Grid Parameters ========
> Using bounding box for grid setup
> Bounding Box Center: 72.000 57.000 42.000
> Xmin, Xmax, Xmax-Xmin: 66.637 76.401 9.764
> Ymin, Ymax, Ymax-Ymin: 50.230 63.667 13.437
> Zmin, Zmax, Zmax-Zmin: 29.381 53.914 24.533
> beginning box center at level 1 72.000 57.000 42.000
> beginning box center at level 2 72.000 57.000 42.000
> Grid dimension at level 1 3 5 7
> Grid origin corrected at level 1 56.000 33.000 10.000
> Grid dimension at level 2 19 21 33
> Grid origin corrected at level 2 62.000 46.000 25.000
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 2.000
>
> What canI do in this regard!
> Any help would be highly appreciated.
>
> Cheers,
> Maryam
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Dec 20 2010 - 06:00:02 PST
