Hi Jason,
The problem persists despite applying patch 5 to AmberTools13 (see below).
I wonder if there is a workaround to the problem. Would an older version of AmberTools work?
Thanks in advance for any advice
George
./update_amber --version
Version is reported as <version>.<patches applied>
AmberTools version 13.23
Amber version 12.21
itvds-ws026:amber12 3i521409$ ./update_amber --update
Preparing to apply updates... please wait.
No new updates available for AmberTools 13
No new updates available for Amber 12
On Feb 26, 2014, at 9:31 PM, George Tzotzos <gtzotzos.me.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 27 2014 - 09:30:02 PST
