that is very helpful. On my test data, I was able to instantaneously
obtain the energy list in a csv file.
thanks again,
Shashi
On Mon, Oct 15, 2012 at 3:42 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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>
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Mon Oct 15 2012 - 13:30:04 PDT
