Hello,
If we run the MPI version of sander and pmemd , we cannot use them in the
serial version of MMPBSA.PY ???
can anyone tell whether we can use them or not??
Did I need to repeat all the steps again??
I cannot upgrade the ambertools 1.5 because i am using LONI ACCOUNT....
Regards,
Vani
On Sun, Apr 10, 2011 at 10:26 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Sun, Apr 10, 2011 at 6:16 PM, vani panguluri <vanipanguluri.gmail.com>wrote:
>
>> Hello,
>>
>> using the serial version of MMPBSA.py i got the following error.
>>
>> ptraj found! Using
>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
>> sander found! Using
>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
>> ptraj found! Using
>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
>> sander found! Using
>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
>> ptraj found! Using
>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
>> sander found! Using
>> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
>>
>
> This tells me that you're still using MPI commands to launch the serial
> version of MMPBSA, so it's launching several MMPBSA.py serial jobs all at
> the same time. This will cause massive problems, as each thread tries to
> write to exactly the same files, and they will be fighting each other.
>
> Review running programs in both serial and parallel to make sure that
> you're doing it properly.
>
>
>> Calculations complete. Writing output file(s)...
>>
>> Error: Sander output is missing values!
>> VDWAALS = ************* EEL = -5060.4993 EGB =
>> -14223.5294NOTE: All files have been retained for
>>
>
> This tells me that your files are incompatible (your prmtop files and
> trajectory files). Make sure that you set up your calculation properly so
> that the complex/receptor/ligand topology files match the generated
> trajectory files (you can check this with visualization programs).
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
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Received on Tue Apr 19 2011 - 20:30:02 PDT
