> On Apr 18, 2016, at 6:47 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com> wrote:
>
> thank you jason
> i found an error while running amber command an its very first time i found this error. i could not find this error that anyone post it any where on search engine :
>
> fareeha.fareeha-HP-ProOne-600-G1-AiO:~/Desktop/amber14$ export AMBERHOME=/home/fareeha/Desktop/amber14
>
> fareeha.fareeha-HP-ProOne-600-G1-AiO:~/Desktop/amber14$ $AMBERHOME/bin/MMPBSA.py -O -i mgbs.in -o FINAL_RESULTS_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y prod.mdcrd
> InputError: Invalid input. Terminate each namelist prior to starting another one.
> Enter `MMPBSA.py --help` for help
As the error message says, your input file is invalid. You need to fix it.
HTH,
Jason
>
>
>> Date: Sun, 17 Apr 2016 12:27:03 -0400
>> From: jason.swails.gmail.com
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] how to embed amber14
>>
>> On Thu, Apr 14, 2016 at 6:34 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
>> wrote:
>>
>>> Hi all,
>>> i want to embed amber Tool 14 in GUI which is python based any one that
>>> can help me how can i embed from amberTool 14 MMPBSA.py for the
>>> calculation of energies. Actually i want to calculate MMPBSA/GBSA by
>>> browsing files not by using command.
>>> How can i embed it in a python based GUI like Boa constructor??
>>
>> By writing code to do that. MMPBSA.py is a command-line utility, as are
>> most of the Amber programs. By reading the MMPBSA.py source code, you
>> should hopefully be able to figure out how to reuse most of the code while
>> embedding it in your program.
>>
>> If you want to use parts of Amber in a custom GUI interface, you will need
>> to grok the various APIs that are available (e.g., pytraj, ParmEd's Python
>> API, sander's Python API, and MMPBSA.py's Python API) and use them in your
>> own GUI-driven programs that you write. This is true of any program out
>> there.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 18 2016 - 04:00:04 PDT
