Hello Jason,
Thank you very much for the clarifications. As an extension of my query (I
should have mentioned this earlier), I am dealing with a protein ligand
complex. I was wondering if the intermolecular interaction energy between
the protein and the ligand is also printed out. of course, this can always
be derived from the energies of the ligand, protein and the complex, but I
was wondering if there is a flag that would print this out.
thanks again,
Shashi
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).
>
> 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 - 13:30:03 PDT
