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.htmuntil 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
> _______________________________________________
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> 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
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Received on Sat Apr 14 2012 - 05:30:03 PDT
