Research:AMOEBA HFE

The script does the automation -- hfe_setup.pl

  You can find the script here /work/oscar/bin

Files you need

(1) xyz file of the ligand

(2) amoeba parameter file

(3) xyz file of water box

(4) AMBER input file template

Procedures

Set-ups

(1) After you run hfe_setup.pl, a prompt pops up

"Enter the xyz file name of the ligand"
Make sure you have that file in your current directory and type in the file name.
The script will figure out how many atoms are there in the ligand and store the range in a "soft_atm.txt" file 
for softcore vdw simulations.

(2) You will then be asked for the parameter file.

(3) Now enter the file name of a waterbox (.xyz)

This is the box you will soak the ligand in. 

(4) "Input the size of the box"

It assumes it is a cubic box, just input the side length in Angstrom.
After this step, a key file will be generated. Also the ligand will be soaked in the waterbox. A new file will be generated.

(5) Electrostatic scaling

 It will ask "Would you like to use the default electrostatic scaling scheme"
 You can either follow the default scheme which is "1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0" by typing "Y" (stands for yes)
 or type in the steps you want for the ele scaling after you type "N"
 The corresponding scaled parameter files will be created.

(6) Van der Waals scaling

 "Would you like to use the default Van der Waals scaling scheme"
 The default is "0.9 0.8 0.75 0.7 0.65 0.6 0.5 0.4 0.2 0  [Y/N]". If you don't like it you can customize the scheme by typing the series of scaling factors
 Similarly, the parameter files will be created.

(7) "Input the mdin file template"

 This will generate a mdin file for equlibration simulation first and later on the mdin for each step.
   
 After this step, all the directories will be created along with the all the files that are needed for amber simulation. 
 A directory for intramolecular simulation will also be created.

Simulations

 The script will launch the equlibration run first after the preparation of all the files. THe time it takes depends on the size of the system.
 Wait until it's done and go to each directory and you will find run.pl file which is the command for simulation.
 Simply do "./run.pl" will fire up your sander simulation.
 

Free energy calculations

 Every directory also contains a "ana" file which will analyze the free energy from the simulation trajectory.
 After all the simulations are finished, run all the "ana" files, this will generate lots of .e energy files
 Once the free energy analysis is over, run "bar". This will yield the free energies between steps.
 

Get the result

 This last step is manual. Open up all the files that "bar" creates and copy paste the free energies for steps into a spreadsheet 
 and get the solvation free energy for your ligand