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
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Received on Thu Jul 05 2012 - 08:00:02 PDT
