[AMBER] AMD parameter: protein residue should count ligand or not

From: Lod King <lodking407.gmail.com>
Date: Tue, 28 Jul 2020 10:55:43 -0700

Hi, amber

I am setting parameters to run AMD.

Should I count the ligand to the 'protein residue" flag in amd input file
or only the total number of protein residues?

Amber manual 18
section 20.2.3 example:

Average Dihedral : 611.5376 (based on MD simulations)
Average EPtot : -53155.3104 (based on MD simulations)
total ATOMS=16950
*protein residues=64*
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Received on Tue Jul 28 2020 - 11:00:04 PDT