Binding Footprint Program

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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)