Kindly assist me in making .psf and .dcd file input for protein network analysis. I want to select Calpha atom for nodes.
For edge assignment, I got this from the manual of Carma package "edges between nodes whose residues are within a cut-off distance (4.5 angstrom) for at least 75% of an MD trajectory".
How can I proceed with this?
Thankx
Vikash Kumar
Hello Pankaj
.psf and .dcd files are generated during the dynamics simulation using NAMD. You will have to convert the trajectory into the dcd format if you have gromacs traj. I will suggest you to use ProDy.
0 votes
0 thanks
- Badges
- Science topic
More Pankaj Mishra's questions See All
Similar questions and discussions