Binding Footprint Program
This program was developed by Noel Carrascal, a former lab member. The program is written in java. The code will take an amber striped trajectory (a traj without waters) and will calculate the the vdw and es binding footprint. That is, the interactions energies in between the each residue and the ligand.
This program has a simple input file always named "input.txt" is in the following formate:
PARM_FILE TRJ_FILE NUMSS START STOP rec RESNUM RESNUM rec RESFIRST RESLAST
a specific example is the following:
active_erlotinib.com.gas.leap.parm active_erlotinib.com.ptraj.stripfit.trj 5000 1 5001 rec 275 275 rec 1 274
In this system, we have 5000 snapshots 274 residues and one ligand (275).
note that all files should be in the same directory
This code currently has a few hard coded values that change from system to system. So in order to run the program, we have a csh script will modify the first input file and will replace the hard-coded variables with the actual values (shown in 2nd input file) uses sed as shown in this example (run.java.csh)