On Mon, Oct 12, 2015 at 9:48 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> Hi,
> Again i download ras-raf_top_mdcrd file and put it in AMBERHOME
This is not where these files go. All of these files should be put *in
the directory you are running the calculations in*.
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y
> ras-raf_top_mdcrd.mdcrd
> [snip]
>
> IOError: Could not open ras-raf.prmtop for reading
>
As Dan mentioned, this means that the file does not exist. So you have
not saved the tutorial files to the directory you are running you
calculations in. Note, you should not run calculations directly in
$AMBERHOME. And Amber never looks for user-supplied input files in
$AMBERHOME -- it looks for them either in the current directory or in the
explicit location given on the command-line. These are concepts in using
command-line programs in Unix generally. It will be very challenging to
use Amber (or any other command-line program in Unix) before mastering the
basics of terminal and command-line use.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 12 2015 - 08:30:04 PDT
