PyMol Trajectory Visualization

PyMol Trajectory Visualization

Visualize Amber nc trajectory in PyMol
I used to convert everything into .dcd file but it is a little complex. Now I found PyMol actually can directly read prmtop & nc file but just need little adjustment.


Rename .prmtop file

rename .prmtop file into .top file.
REF:

https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Loading_AMBER_prmtop_and_inpcrd_files_into_Pymol

load top file and nc file

load AAA.top
load_traj BBB.nc, AAA

Note if want to use .mdcrd file from Amber, it needs be renamed as .trj before loading

REF:

https://pymolwiki.org/index.php/Load_traj
https://sourceforge.net/p/pymol/mailman/message/36374096/
https://sourceforge.net/p/pymol/mailman/message/35166151/