Re: [AMBER] MMPBSA error in segmentation fault

From: Aditya Setiajid <>
Date: Sat, 14 Apr 2012 14:03:28 +0800 (SGT)

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 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 <> To: Aditya Setiajid <>; AMBER Mailing List <> 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 that was released with AmberTools12 ( -Bill On Fri, Apr 13, 2012 at 4:05 AM, Aditya Setiajid <> 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 --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 -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 > > > -- 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
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