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--- interaction_energy_of_ligand_in_charmm [2021/09/01 09:37] – edit
+++ interaction_energy_of_ligand_in_charmm [2022/01/12 10:17] (current) – edit
@@ Line 1: / Line 1: @@
 This is a tutorial on how to calculate the interaction energy and it is worth noting that there was help from other sources such as a template code on the Charmm source codes website by Lennart Nilsson.
 Begin by downloading the source files {{ :inte.tar.gz |}}
 **It is important to re-center the trajectory so that system is always in the center. There is a way to check if everything works by averaging together the total interaction energy, total electrostatic, and total VdW energies and seeing if the sum of the average of VdW+ average ELEC=average(ENER)**
+To re-center the trajectory examine the recenter_2 folder and look specifically at the recenter1.inp recenter2.inp recenter3.inp and adjust the selection to the specific need. This case is examining a dimer PROA and PROB and both are re-centered.
+Run them by typing
+     ./recenter1.scr
+     ./recenter2.scr
+     ./recenter3.scr
+Alternatively something similar can be done by adding these lines somewhere between the traj read and the inte command lines
+     coor stat sele segid PROA .or. segid PROB end
+     coor tran xdir -?XAVE ydir -?YAVE zdir -?ZAVE
+     energy
+Then adjust the path in the interaction energy script to access the new translated dimer system that is centered.
 This script is used to calculate the per/residue interaction energies over several trajectories. Each loop that is incorporated into the code slows everything down a lot and that is why the charmm script has to be invoked individually for each residue and again for each trajectory file and then combined using linux.
@@ Line 62: / Line 80: @@
      inte sele segid CARA .and. resid @id end sele segid PROA .or. segid PROB end
+ __Tabulating the Data__
+Author: Shyam Patel
+    - Download {{ :IntEnergyComplexTab.py.zip |}}
+    - Next, uncompress and upload the .py file to your directory and uncompress the python file. Move it to one directory outside of the range of directories you wish to tabulate. Replace startDir and endDir with the number component of the directories you wish to run the script over. Update the dir variable with anything else that may be in your directory name. Then update the fileBase variable to the name of the files you wish to tabulate in each directory (i.e inter_NUM.dat).
+    -After, activate your anaconda environment (if you don't have anaconda installed, go to the anaconda page for linux and download it your home directory).
+        conda activate NAME OF ENVIRONMENT
+- If you do not have numpy or pandas installed run pip3 install numpy and pip3 install pandas (assuming you are using python3)
+- then run python3 IntEnergyComplexTab.py
+        pip3 install numpy
+        pip3 install pandas
+        python3 IntEnergyComplexTab.py