[AMBER] query on a script called getdvdl.py in AMBER TI tutorial section

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Sat, 8 Feb 2020 14:50:39 +0000

Hi All,

‚ÄčI have some queries on a script found on " http://ambermd.org/tutorials/advanced/tutorial9/#analysis "
There is a analysis folder inside the A9 directory and it has a script called analyse.csh
The contents are as follows:

#!/bin/sh


top=$(pwd)
getdvdl=$top/getdvdl.py

for system in ligands complex; do
  cd $system
  result=0.0

  for step in decharge vdw_bonded recharge; do
    cd $step

    python $getdvdl 5 ti001.en [01].* > dvdl.dat
    echo -n "$system/$step: "
    dG=$(tail -n 1 dvdl.dat | awk '{print $4}')
    echo $dG
    result=$(echo $dG + $result | bc)

    cd ..
  done

  echo '--------------------------------'
  echo "dG sum for $system = $result"
  echo

  cd $top
done

The getdvdl.py can be found at A9/ligand/pmemd/free_energy location once you have the A9.tar.gz file downloaded from the amber link I sent


I have 3 questions:

  1. I have done the decharge, vdw, steps together and so, will I just feed the script one folder, instead of for steps in x,y,z...?
  2. I am not a python programmer and I I am having a hard time analysing what the arguments are for getdvdl.py ?python $getdvdl 5 ti001.en[01]*

does it require mden files as input for the program?
Also what is the 5 in the argument?
any help or any ideas on how to go about it will be very useful.

Thanks








Debarati

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Received on Sat Feb 08 2020 - 07:00:03 PST
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