Hi Jason,
I’ve tried the same on a different machine. The same error appears (single HOH molecule included in the protein topology). I’m attaching the log and the mdout.
I checked for patches and none was found. I made clean, re-configured and reinstalled. The results are shown below. I hope this helps you to troubleshoot the problem.
Many thanks
George
PROCEDURE
In /amber12, I run <make clean> and run ./configure -mpi gnu
I also checked for patches
$AMBERHOME/update_amber --check
Checking for available patches online. This may take a few seconds...
Available AmberTools 13 patches:
No patches available
Available Amber 12 patches:
No patches available
I run test.parallel and got the results shown below.
make[2]: Target `test.parallel2' not remade because of errors.
517 file comparisons passed
2 file comparisons failed
0 tests experienced an error
Test log file saved as /Users/georgios.tzotzos/Programs/amber12//logs/test_amber_parallel/2014-02-26_20-39-52.log
Test diffs file saved as /Users/georgios.tzotzos/Programs/amber12//logs/test_amber_parallel/2014-02-26_20-39-52.diff
Summary of AmberTools parallel tests:
43 file comparisons passed
1 file comparisons failed
0 tests experienced errors
On Feb 26, 2014, at 7:13 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Feb 26, 2014 at 3:18 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Apologies to burden the list with this problem.
>>
>> I've run MMPBSA.py.MPI on a different simulation. I encountered the same
>> problem. Please see attached mdout and log files.
>>
>> I wonder if I should recompile and run MMPBSA again.
>>
>> Your suggestions will be most welcome.
>>
>
> I downloaded your files and tried them out. I did get an error with
> cpptraj when I tried to compute the surface area using LCPO (which is the
> default surface area method) with an error message:
>
> Error: Atom 2016 in mask :* does not belong to solute.
>
> Warning: Setup failed for [surf thing :* out test.dat]: Skipping
>
> ----- 4fqt_OVT.inpcrd (1-1, 1) -----
>
> 100% Complete.
>
> This occurs because including solvent in a surface area calculation is
> unusual, and this is a check in cpptraj to prevent a mistake. (Your
> topology file has a WAT residue.) This issue was addressed by update.5 for
> AmberTools 13 (see http://ambermd.org/bugfixesat.html). Can you check that
> these bug fixes are applied and recompile AmberTools?
>
> If it still doesn't work, I think I'm going to need to be able to reproduce
> this error locally on one or two frames.
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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Received on Wed Feb 26 2014 - 17:00:03 PST
