[Dock-fans] ligand -regding

Vinay Kumar ksvinaykumar at gmail.com
Sat Dec 1 21:25:56 PST 2007


Hello dockers,

I would like to know,
1) why is it that only polar hydrogens are added in the macromolecule?
2) if we need to add all hydrogens (polar and non-polar) explicitly to
the ligand while a docking is performed? for ex- if the ligand is
phenol, do i have to draw the phenyl ring with CH2 explicitly shown,
or just use the ring structure provided by the drawing interface?

would like your thoughts,

regards,
Vinay


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