DelPhiForce is a tool to calculate electric field, forces, energy for a two molecule system. The electrostatic forces are able to be visualized in VMD. In the DelPhiForce/bin folder, there are several files:

DelPhiForce.sh 
ForceGen.sh 
draw_arrow.tcl

The usage of DelPhiForce is:

./DelPhiForce.sh file1 file2 output_name

file1 is the reference molecule, file2 is the probe molecule, output_name is the output file name.

Here is an example of using DelPhiForce on a dynein-tubulin complex on Linux or Mac system. Once DelPhiForce.tar.gz is downloaded, the example can be found in the DelPhiForce/example/ folder. This example is the dynein MTBD (microtubule binding domain) and tubulin complex. The dynein MTBD is detached from tubulin and rotated in 90 degrees. The goal is to calculate and visualize the electrostatic forces on all the residues of dynein MTBD. To run the example, go to the example folder, copy all files from the DelPhiForce/bin/ folder to DelPhiForce/example/ folder, then run DelPhiForce by the command:

./DelPhiForce.sh 3j1t_tu.pqr 3j1t_dy_90.pqr out

After the run, you will get such files: out.residue out.residue is the result for electrostatic forces on all the residues of dynein MTBD; out.atom out.atom is the result for electrostatic forces on all the atoms of dynein MTBD; out_residue.tcl out_residue.tcl is generated for visualization of electrostatic forces on residues of dynein MTBD in VMD. out.tcl out.tcl is generated for visualization of the total electrostatic force of dynein MTBD in VMD.

In order to visualize the forces, first launch VMD, open the molecules of 3j1t_dy_90.pqr. In the VMD TkConsole, run the commands:

source draw_arrow.tcl
source out_residue.tcl 
source out.tcl

Then open the molecule 3j1t_tu.pqr in VMD.

The electrostatic forces are displayed as shown in figure 1. Each arrow illustrates an electrostatic force on a residue of dynein MTBD. The tail of an arrow is the mass center of the corresponding residue. The length of an arrow indicates the magnitude of the force. Figure 1. Electrostatic forces of residues of dynein generated by DelPhiForce.

Contact:

Li, Lin, Arghya Chakravorty, and Emil Alexov. "DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding." Journal of Computational Chemistry 38.9 (2017): 584-593.

https://doi.org/10.1002/jcc.24715