it appears that the variable keep_files should be set to 2 to keep the
temporary files. Nevertheless, I would still be interested to know the
energy values associated with individual frames can be listed.
thanks,
shashi rao
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
>
> 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
>
>
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Mon Oct 15 2012 - 13:00:03 PDT
