[AMBER] details of energy values for individual frames in MMPBSA.py calculations...

From: Shashidhar Rao <shashidharr.gmail.com>
Date: Mon, 15 Oct 2012 15:12:41 -0400

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

While the job was successfully completed, the output file
(FINAL_RESULTS_MMPBSA.dat) only seems to report the average energy values
over the five frames of the trajectory I chose. I would like to know if
there is a way by which I can get the same information for all the
individual frames, preferably in a format that can be used in excel to
generate plots. Also I would like to know where the intermediate files are
saved. if they are automatically cleaned up, is there an option to prevent
the clean-up or to effect only partial clean-up.

thanks,
shashi


-- 
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com



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Received on Mon Oct 15 2012 - 12:30:09 PDT
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