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--- interaction_energy_of_ligand_in_charmm [2021/08/30 00:23] – 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 |}}
-This script is used to calculate the per/residue interaction energies over several trajectories. Each loop that is incorporated into the code slows everything do 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.
+**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.
 __The .scr file__
@@ Line 28: / Line 48: @@
   * The input file is what CHARMM reads and tells CHARMM what to do
   * dimension maxres 150000 needs to be at the top of the input file to override the limits for large simulations
-  * The lines below are standard to load the files of the system and set the number of frames in the .dcd file adjust as needed. It can be found by loading the .psf and then .dcd file into vmd and seeing the number of frames in one single .dcd file (note that it starts at 0 so add one)
+  * The lines below are standard to load the files of the system and set the number of frames in the .dcd file adjust as needed. It can be found by loading the .psf and then .dcd file into vmd and seeing the number of frames in one single .dcd file (note that it starts at 0 so add one) if it is different from 200 then the time tracker needs to be recalibrated as well at the bottom of the input file
   * Copy the updated parameter files to the local directory and update the .psf and .crd files by copying replacing them in the local directory or adjust the location in the psfcrd, update the cryst.str file with the updated dimensions of the simulation based off the last simulation in the file dyn???.xsc.gz using the reference positions of the three bold numbers below as the x, y, and z dimensions
@@ Line 41: / Line 61: @@
   - Update the path to the .dcd files
      open unit 1 read file name "/lustre/rallsopp/glucoM4/namd/dyn"@k".dcd"
+This section below should be updated from the charmm directory, one directory above the namd directory in the step5_production.inp or the step7_production.inp, with the @fftx ... being replaced with the numbers in the checkfft.str file in the same directory
+     fftx @fftx ffty @ffty fftz @fftz
+     nbonds atom vatom vfswitch bycb -
+            ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 -
+            inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
+            ewald pmew fftx 120 ffty 120 fftz 120  kappa .34 spline order 6
+     energy
+  - Finally it is time to check over the selection of the receptor and the ligand. It is crucial to look over the .pdb, .psf, .crd files and know the different call names to select the different components of the system. For instance as of 2021 a protein/peptide A shows up as "PROA" and a carbohydrate ligand chain is named "CARA", if there are multiple it would be "CARA", "CARB", "PROB"
+  - Start by selecting the first residue of the polysaccharide or peptide using the @id command to substitute in the correct number and then select the receptor, if there are multiple that are interacting it is possible to select them all with the .or. to include multiple. And it is also possible to do more specific analysis of the receptor by specifying individual residues there as well.
+     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