This directory contains all necessary files to run a flexible LMOD
docking calculation where the ligand and all contact protein residues
are fully flexible. This example very closely reproduces the results in
the following recent publication:

Natural Apocarotenoids and Their Synthetic Glycopeptide Conjugates 
Inhibit SARS-CoV-2 Replication
Pharmaceuticals 2021, 14, 1111.
https://doi.org/10.3390/ph14111111

The open article and supplementary material are included in the doc sub-
directory. There are 3 work directories: xmin, lmod, and vib. The 
Run_xmin script minimizes the whole system and the Run_lmod-dock script 
runs the flexible docking calculation where non-contact protein residues 
are restrained and the ligand is tethered to the binding site but 
otherwise fully flexible and free to translate and rotate. The 
Run_lmod-vib script computes the same vibrational modes that the 
docking calculation utilizes, and is useful in visualizing the modes. In
general, it is always a good idea to visualize the vibrational modes 
before running any LMOD calculation. Also note that in case part of the 
system is frozen/restrained the vibrational modes are not necessarily 
"natural" but always represent concerted atomic movements that can 
efficiently explore conformational space. LMOD has numerous parameters, 
please consult the Amber User Manual, but the settings in these example 
scripts are quite robust.

Note: The primary results of the LMOD calculation are stored in the file
lmod-dock_conflib, to transform that to dcd file use 'cpptraj -p 
system.parm7 -y lmod-dock_conflib -x system-dock-poses.dcd'

There are two Pymol sessions vib/system-vibmodes.pse and 
lmod/system-docking-poses.pse showing the modes and docking poses, 
respectively. See the LMOD-sander-vibmodes-example for details how these
Pymol sessions were created.

For any type of LMOD calculation always process the original parameter 
file in parmed, executing the 'lmod' command.
