Hello,
Here is where I will suggest using ante-MMPBSA.py (as long as you are using
AmberTools 12). This version is robust and should work with any normal
Amber topology file (i.e., not CHAMBER topologies). You can use
ante-MMPBSA.py to generate compatible topology files.
Another common problem is that strip_mask is set improperly. Make sure
that you are stripping _all_ atoms that are in your solvated system but
that are not in your topology files (specifically, watch out for ions!).
The benefit of ante-MMPBSA.py is that it it takes 2 masks: strip_mask and
either receptor_mask or ligand_mask. These are the same masks that you can
pass to MMPBSA.py to get the appropriate behavior. (Again, be careful
about ions)
HTH,
Jason
On Sun, Apr 15, 2012 at 9:56 AM, Aditya Setiajid <setiajid11.yahoo.com>wrote:
> 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.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
> >>_______________________________________________
> >>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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 15 2012 - 08:00:02 PDT
