[Dock-fans] positive energy with water molecule

[Anuradha Mittal]

Hi Dock users,

I am carrying out amberdock recoring calculations on a set of ligands. There
is a water molecule in the protein that I need to include while performing
the calculations.

I am getting positive amber score for all the ligands. However if I remove
that water molecule all scores are negative. I prepared all structures using
sybyl but did change the nomenclature according to amber.

What am I doing wrong here? Is it that Amber-dock doesn't support water
molecules? Or do I need to explicitly define the parameters for water? Any
suggestions?


Thanks

Anu
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