These tests are the basic benchmarks that we use to make sure that the code
works. Since MMPBSA.py is really just a script that organizes data and
external program calls, the important thing is to diagnose the issues with
the external programs.
My suggestion is to recompile AmberTools 12 (run "make clean uninstall"
from $AMBERHOME and then re-run configure and make install). Then, run the
test suites to make sure that you are not getting a lot of test failures.
See
http://jswails.wikidot.com/installing-amber12-and-ambertools-12#toc11 for
more details. You should wait until the tests pass before attempting
normal simulations.
HTH,
Jason
On Thu, Jul 5, 2012 at 10:32 AM, qiqi <hova.1985.yahoo.com.cn> wrote:
> Hi Jason,
>
> The test was run as "make test.mmpbsa", no
> "test.mmpbsa_py " is found in the makefile.
>
> The test failed in PB part.
> Here are the information got from the test.
>
> ********************************
> nice make test.mmpbsa
>
> cd mmpbsa_py && make test
>
> make[1]: Entering directory
> `/shared/build/amber12/AmberTools/test/mmpbsa_py'
>
> cd EstRAL_Files && ./Run.makeparms
>
> diffing com.top with c.top
>
> PASSED
>
> ==============================================================
>
> diffing rec.top with r.top
>
> PASSED
>
> ==============================================================
>
> diffing lig.top with l.top
>
> PASSED
>
> ==============================================================
>
> cd 01_Generalized_Born && ./Run.GB
>
> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
>
> PASSED
>
> ==============================================================
>
> diffing energies.csv.save with energies.csv
>
> PASSED
>
> ==============================================================
>
> cd 02_Poisson_Boltzmann && ./Run.PB
>
> ./Run.PB: Program error
>
>
>
>
>
> ok, so that is a problem. looking at
> /shared/build/amber12/AmberTools/test/mmpbsa_py/02_Poisson_Boltzmann/mmpbsa.out
>
>
>
> Reading command-line arguments and input files...
>
> Loading and checking parameter files for compatibility...
>
> mmpbsa_py_energy found! Using
> /shared/build/amber12/AmberTools/bin/mmpbsa_py_energy
>
> cpptraj found! Using /shared/build/amber12/AmberTools/bin/cpptraj
>
> Preparing trajectories for simulation...
>
> 2 frames were processed by cpptraj for use in calculation.
>
>
>
> Beginning PB calculations with
> /shared/build/amber12/AmberTools/bin/mmpbsa_py_energy
>
> calculating complex contribution...
>
> File "/shared/build/amber12/AmberTools//bin/MMPBSA.py", line 565, in ?
>
> external_progs, '_MMPBSA_', normal_system)
>
> File "/shared/build/amber12/bin/MMPBSA_mods/calculation.py", line 174,
> in run_calculations
>
> calc.Run(stdout=os.devnull)
>
> File "/shared/build/amber12/bin/MMPBSA_mods/calculation.py", line 395,
> in Run
>
> raise CalcError('%s failed with prmtop %s!' % (self.program,
>
> CalcError: /shared/build/amber12/AmberTools/bin/mmpbsa_py_energy failed
> with prmtop ../EstRAL_Files/com.top!
>
> Exiting. All files have been retained.
>
> *******************************************
>
> It will be great if you can give me some advice about what is the error
> message about.
> Thank you very much for your help!
>
> All the best,
> Qi
>
>
>
>
>
> --- 12年7月4日，周三, Jason Swails <jason.swails.gmail.com> 写道：
>
> 发件人: Jason Swails <jason.swails.gmail.com>
> 主题: Re: [AMBER] Problem while running MMPBSA
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2012年7月4日,周三,上午11:31
>
> On Mon, Jul 2, 2012 at 3:37 PM, qiqi <hova.1985.yahoo.com.cn> wrote:
>
> > Hi Jason,
> >
> > Thank you very much for your reply.
> > I did use the tutorial data to do the test calculation.
> >
> > I am running the calculation using AmberTools12 and Amber11.
> > I think it only call the AmberTools12 in my GB/PB test calculation,
> right?
> > Here are the information you mentioned.
> >
>
> Yes, it only uses AmberTools 12. In fact, it will refuse to use any Amber
> 11 programs unless you put "search_path=1" in the &general section of the
> input file. Since you didn't, and there were no complaints about missing
> programs, it did not try to use Amber 11.
>
>
> >
> > [root.moldyn ~]# uname -a
> > Linux moldyn 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:10:13 EDT 2011
> x86_64
> > x86_64 x86_64 GNU/Linux
> > [root.moldyn ~]# mpicc -V
> > Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R)
> > 64, Version 12.0.0.084 Build 20101006
> > Copyright (C) 1985-2010 Intel Corporation. All rights reserved.
> >
>
> This is weird. I have more or less the same compiler suites (12.0.1 and
> 12.0.3) on the same architecture (x86_64), and I had no issues. Do the
> AmberTools 12 MMPBSA.py tests pass?
>
> All the best,
> Jason
>
> --
> 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
> _______________________________________________
> 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 Thu Jul 05 2012 - 08:30:04 PDT
