AMBER Archive (2007)

Subject: AMBER: Parse charges for small molecules

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Wed Aug 22 2007 - 23:50:38 CDT

 Hi,

I am trying to carry out mm-pbsa simulations using amber 9 and want to use
delphi for PB calculations. The ligand is highly anionic in nature with
sulfate groups. I have previously derived partial charges using G98 quantum
mechanics methods.

I can assign parse charges to the protein but I have no clue what charges
should I use for the ligand. How can I assign charges to the ligand for
delphi calculations in .crg file? Should I use the same partial charges to
the ligand for performing mm-pbsa simulations?

Regards,
Neha Gandhi,
Curtin University of Technology

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