Hi everyone,
I have installed MPICH-3.1.4 and latest version of Amber19. The MMPBSA.py.MPI has been tested without any problem.
Maybe the MPICH-3.3 could not be compatible with the latest version of Amber 18 or 19.
Thank you very much!
Best regards.
Lei
> 在 2019年8月18日，上午10:56，Lei Zhao <jackyzhao010.gmail.com> 写道：
>
> Hi David,
> Thank you for your suggestions. I have solved this problem. I have tested MMPBSA.py to calculate the binding energy without any problem. Thus, I think that the MPICH 3.3 could not be compatible with the latest version of amber. I have recompiled the MPICH-3.1.4 and reinstalled the Amber18 to solve this problem.
>
> Thank you very much for your suggestions.
>
> I am wondering the latest version of MPICH could not be suitable for the latest version of amber.
>
> Now, I am compiling Amber19 with MPICH-3.1.4. When I have finished it, I will report the results below.
>
> Thanks a lot.
>
> Best regards,
>
> Lei
>
>> 在 2019年8月17日，下午9:11，David Case <david.case.rutgers.edu> 写道：
>>
>>> On Sat, Aug 17, 2019, jacky zhao wrote:
>>>
>>> I have recompiled the latest amber18 to test MMPBSA.py.MPI. However,
>>> the similar error can be found. I have also used our previous MD
>>> trajectory to test the MMPBSA.py.MPI. Previously, this MD trajectory
>>> can be calculated by amber18 without any problem.
>>>
>>> I am wondering why cpptraj could not reach the complex topology
>>> file. All these topology files were generated by ante-MMPBSA.py.
>>
>> Have you tried running a short MMPBSA.py calculation with the serial version
>> of the code? What happens with that? What happens if you run MMPBSA.py.MPI
>> with just 2 threads (rather than 45)?
>>
>> If this sort of debugging doesn't help, it seems to me that you will need to
>> create a small example that illustrates the problem.
>>
>> ....dac
>>
>>
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Received on Sat Aug 17 2019 - 22:30:02 PDT
