HITS-MBM/gromacs-fda

Network Representation of Force Distribution

KhushSingh opened this issue · 2 comments

KhushSingh commented

Hi, Bernd!

I conducted (TR)FD analysis to investigate the effect of a mutation on the force propagation within a protein-ligand complex. Now, I need to generate images for my publication highlighting the difference in the force distribution from the point of mutation between wild-type and mutant protein. I was hoping to generate a network representation of the force distribution within the protein, a figure similar to the one attached, Fig 2 (C). My figure looks very different (attached); the image was generated using .pfa and pf_draw package within VMD 1.9.1 as suggested in the manual.

It would be of great help if you could advise me on how to obtain network representation of force distribution from a particular residue.

figure c_fda

trfda

BerndDoser commented

Hi KhushSingh,

Please take a look to the analysis modules in the documentation chapter 5. Fig 2(C) looks to me like such a graph.

Best regards,
Bernd

BerndDoser commented

Please reopen the issue or create a new one in case of more questions.