Hi All,
I 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
