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.

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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

useful commands in visualization

intra_fit AAA

https://pymolwiki.org/index.php/Intra_fit

visualize cavity

set surface_cavity_mode, 2

https://www.biochemistry.ucla.edu/Faculty/Hubbell/protocols/Displaying%20cavities%20with%20PyMOL.pdf

Set cutoff to only display large cavities

set cavity_cull, <float>

The float number is approximately in a unit of Ang^3
https://pymolwiki.org/index.php/Cavity_cull

The cavities are carved by scanning the protein surface with two different solvent radius, the can be set via

set surface_cavity_radius, <float>
# and
set surface_cavity_cutoff, <float>

They works as something like:

Small Probe (surface_cavity_radius):
    ○ ○ ○ ○ ○ ○ ○ ○ ○
  ○ ○ ○ ███████ ○ ○ ○ ○
○ ○ ○ ███████████ ○ ○ ○
○ ○ ███████████████ ○ ○    
○ ○ ███████████ ○ ○ ○ ○   <- Can access smaller spaces
○ ○ ███████████████ ○ ○
○ ○ ○ ███████████ ○ ○ ○
  ○ ○ ○ ███████ ○ ○ ○ ○
    ○ ○ ○ ○ ○ ○ ○ ○ ○

Large Probe (surface_cavity_cutoff):
    ● ● ● ● ● ● ●
  ● ● ● ███████ ● ● ●
● ● ● ███████████ ● ● ●
● ● ███████████████ ● ● 
● ● ███████████     ● ●   <- Cannot access smaller spaces
● ● ███████████████ ● ●
● ● ● ███████████ ● ● ●
  ● ● ● ███████ ● ● ●
    ● ● ● ● ● ● ●

Cavity
               ░░░░       <- Detected cavity

REF:

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