AMBER: Parse charges for small molecules

From: Neha Gandhi <>
Date: Thu, 23 Aug 2007 12:50:38 +0800


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?

Neha Gandhi,
Curtin University of Technology

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Received on Sun Aug 26 2007 - 06:07:19 PDT
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