Dear Amber Users !
Dealing with the analysis of protein-ligand system I am using the following
script to
# 1 - calculate distance of the ligand from the residue involved in the
interaction
distance lig-glu166 :lig :166.N out distanceLIG.xvg
# 2 - calculate number of hydrogen bonds between ligand and protein
hbond contacts :1-300|:lig out hydrogenbonds.xvg nointramol
My question is it possible
1 - calculate distance taking into account initial position of the ligand
and the position during the simulation (without definition of the active
site residue ) ?
2 - calculate the number of hydrogen bonds between ligand and all residues
around 10 A from the ligand (so providing only a geometrically-based amber
mask without explicit definition of any selection related to number of
amino acids of protein) ?
Many thanks in advance !
Enrico
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Received on Mon Jul 15 2024 - 08:00:02 PDT
