Dear Bill and Amber Users,
I have visualized all three trajectories made from MMPBSA.py with the corresponding prmtop files with VMD, and the visual was totally messed up..
it was different when i visualized all four trajectories from prmtop and inpcrd files that created by tLeap with VMD (i visualized the prmtop and inpcrd files before running minimization, after minimization and after production) and it was visualized correctly as be supposed..
What's wrong with my prmtop files? Thank you for you advice, I'm very need your help..
Best Regards,
Muhammad Aditya Setiajid
University of Indonesia
----- Forwarded Message -----
From: Bill Miller III <brmilleriii.gmail.com>
To: Aditya Setiajid <setiajid11.yahoo.com>
Cc: "amber.ambermd.org" <amber.ambermd.org>
Sent: Saturday, April 14, 2012 7:07 PM
Subject: Re: [AMBER] MMPBSA error in segmentation fault
Can you visualize all three trajectories made from MMPBSA.py (i.e. _MMPBSA_receptor.mdcrd, etc) with the corresponding prmtop files for your system?
-Bill
On Sat, Apr 14, 2012 at 2:03 AM, Aditya Setiajid <setiajid11.yahoo.com> wrote:
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
>
>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
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Received on Sun Apr 15 2012 - 07:00:03 PDT
