This directory contains all necessary files to run a LMOD loop search 
calculation where the protein is restrained and only the loop in 
question is free to move. This example optimizes the geometry of a FAB 
fragment loop that is involved in antibody maturation.

There are 3 work directories: xmin, lmod, and vib. The Run_xmin script 
minimizes the whole system and the Run_lmod-loop-search script 
runs the loop optimization. The Run_lmod-vib script computes the same 
vibrational modes that the loop search 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-loop_conflib, to transform that to dcd file use 'cpptraj -p 
FAB.parm7 -y lmod-loop_conflib -x FAB-loop-confs.dcd'

There are two Pymol sessions vib/FAB-loop-vibmodes.pse and 
lmod/FAB-loop-confs.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.
