On Mon, Oct 15, 2012 at 3:40 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Mon, Oct 15, 2012 at 3:12 PM, Shashidhar Rao <shashidharr.gmail.com>wrote:
>
>> Hello,
>>
>> I am attempting to run MMPBSA calculations on a set of protein-ligand
>> complexes obtained from MD trajectories. I have attached the input file
>> that I used for such a computation. As a test, I selected the first five
>> frames with the verbosity level of 2. The command I used looked like
>> this:
>>
>> MMPBSA.py -O -i mmpbsa_input1 -cp 3LFF_Z83complex_nowat_noCI.prmtop -rp
>> 3LFF_receptoronly.top -lp Z83ligand.top -y test1_nobox.nc
>
>
> Add the flag "-eo <file_name.csv>" and it will dump a CSV file
> (comma-separated-values) with exactly the information you want.
>
> CSV files are read natively by excel and other spreadsheet programs.
> keep_files=2 is unnecessary (default keep_files is 1).
>
Also, you should be able to use the flag "-rewrite-output" to avoid
re-running simulations. So in the directory with your output files run:
MMPBSA.py -rewrite-output -eo energies.csv
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 15 2012 - 13:00:06 PDT
