Dear Bill and Amber Users,
I have already used AmberTools12 right now, and i have already did the tutorial AMBER ADVANCED TUTORIALS
TUTORIAL 3 - SECTION 3.2
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm until i got the FINAL_RESULTS_MMPBSA.dat which means my AmberTools dosn't have any problem with MMPBSA and MMGBSA.. I think the problem come from my .prmtop input..
here i attached my _MMPBSA_receptor_gb.mdout and MMPBSA.log
I didn't see any error message in the _MMPBSA_receptor_gb.mdout, there was just stopped when reading the first frame in receptor mdout..
Is there any problem in my receptor.prmtop?
Best Regards,
Muhammad Aditya Setiajid
University of Indonesia
________________________________
From: Bill Miller III <brmilleriii.gmail.com>
To: Aditya Setiajid <setiajid11.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, April 13, 2012 7:48 PM
Subject: Re: [AMBER] MMPBSA error in segmentation fault
Are there any error messages in the _MMPBSA_receptor_gb.mdout?
I would also suggest upgrading to the newest version of MMPBSA.py that was released with AmberTools12 (
http://ambermd.org/#AmberTools)
-Bill
On Fri, Apr 13, 2012 at 4:05 AM, Aditya Setiajid <setiajid11.yahoo.com> wrote:
Dear Amber Users,
>
>I faced a problem when i ran MMPBSA with my own protein and ligand after 200ps MD simulation. I just want to try if my way to run MMPBSA is right or not, apparently my job didn't worked. This error message appeared when i ran MMPBSA.
>
>Reading command-line arguments and input files...
>Loading and checking parameter files for compatibility...
>ptraj found! Using /home/farm/mirror/Programs/amber/amber11/bin/ptraj
>mmpbsa_py_energy found! Using /home/farm/mirror/Programs/amber/amber11/bin/mmpbsa_py_energy for GB calculations
>mmpbsa_py_energy found! Using /home/farm/mirror/Programs/amber/amber11/bin/mmpbsa_py_energy for PB calculations
>Preparing trajectories for simulation...
>20 frames were read in and processed by
> ptraj for use in calculation.
>
>Beginning GB calculations with mmpbsa_py_energy...
> calculating complex contribution...
> calculating receptor contribution...
>Segmentation fault
>Error: mmpbsa_py_energy error during GB calculations!
>NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
>
>
>What's wrong with my job? what is the meaning of segmentation fault? here is my command to run MMPBSA:
>
>nohup MMPBSA -O -i MMPBSA.in -o 6COX_s58k_MMPBSA.dat -sp 6COXAsolvoct.prmtop -cp 6COXSVak_netral.prmtop -rp 6COXSonly.prmtop -lp s58k.prmtop -y 6COXAsolvoct_md2_ntpr2.crd > MMPBSA.log &
>
>
>
>Best Regards,
>Muhammad Aditya Setiajid
>University of Indonesia
>_______________________________________________
>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 Fri Apr 13 2012 - 23:30:02 PDT
