Hi,
this is running on gnu cluster on serial installation, I found that for the first problem when i set igb=1, MMGBSA is running, but when it is set igb=5, it shows the error
File "/ghome/atyagiaa/amber14/bin/MMPBSA.py", line 96, in <module>
app.run_mmpbsa()
File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
self.prmtop))
CalcError: /ghome/atyagiaa/amber14/bin/sander failed with prmtop complex.prmtop!
Exiting. All files have been retained.
for the second problem: I have followed the installation guide as follows:
./configure -mpi gnu
make install
export DO_PARALLEL='mpirun -np 16’
make test.parallel
everything finished fine, but when I had checked AMBERHOME/bin/ their is no MMPBSA.py.MPI file in the folder.
what could be the reason
Thanks in advance
Abhi
~
> On 27 Mar, 2015, at 3:00 am, amber-request.ambermd.org wrote:
>
> ------------------------------
>
> Message: 15
> Date: Thu, 26 Mar 2015 08:55:35 -0400
> From: Kenneth Huang <kennethneltharion.gmail.com <mailto:kennethneltharion.gmail.com>>
> Subject: [AMBER] MMGBSA error
> To: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org>>
> Message-ID:
> <CALeh7kBoAEw+CLHBu6USEDxeRu6wYW98Wjy_tyvOnpNpfrLhXA.mail.gmail.com <mailto:CALeh7kBoAEw+CLHBu6USEDxeRu6wYW98Wjy_tyvOnpNpfrLhXA.mail.gmail.com>>
> Content-Type: text/plain; charset=UTF-8
>
> Abhi,
>
> What's the exact error it's giving on the GPU cluster? And have you checked
> the _MMPBSA_complex_gb.mdout file to see if there's a description of
> what's specifically going wrong?
>
>
> For your second problem, I'm guessing it's because you haven't compiled
> Amber in mpi- you can use the below in the Amber directory.
>
> ./configure -mpi gnu
> make install
>
> Best,
>
> Kenneth
>
> On Thu, Mar 26, 2015 at 2:06 AM, Abhishek TYAGI <atyagiaa.connect.ust.hk <mailto:atyagiaa.connect.ust.hk>
> <javascript:_e(%7B%7D,'cvml','atyagiaa.connect.ust.hk <mailto:atyagiaa.connect.ust.hk>');>> wrote:
>
>> Hi,
>>
>>
>> I have following questions:
>>
>>
>> 1. I am using MMGBSA for receptor-ligand interaction, the calculations
>> successfully finished on my PC, but when i tried on GPU cluster, I was not
>> able to run it, for the similar files, it shows error for complex.
>>
>>
>> 2. Second problem is with mpi, i had installed on the gpu cluster
>> following the installation guidance provided in the Amber manual, and I
>> have not found MMPBSA.py.MPI on my bin directory.
>>
>>
>> Could anyone suggest me what could be the error
>>
>>
>> Thanks? in advance
>>
>>
>> Abhi
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>>
>
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Received on Fri Mar 27 2015 - 10:00:05 PDT
