hi,
I again install amber14 and AmberTools 15 after changing directory now at this time i could not find "inputparse.py" python script i don't know why it is missing at this time?
how can i find it to place it in $AMBERHOME/bin
i was the following commands for installation of ambertools
cd Downloads/amber14
export AMBERHOME=/home/ayesha/Downloads/amber14
./configure gnu
source /home/ayesha/Downloads/amber14/amber.sh
make install
export LD_LIBRARY_PATH=$AMBERHOME/lib\:$LD_LIBRARY_PATH
cd $AMBERHOME/AmberTools/src/mmpbsa_py
regards
ayesha kanwal
> Date: Mon, 12 Oct 2015 11:12:35 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
>
> 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 - 21:30:03 PDT
