AMBER Archive (2008)

Subject: AMBER: MM-PBSA

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Wed Jun 18 2008 - 02:37:33 CDT

Dear Amber users,

I am using single trajectory method for mm-pbsa analysis as
implemented in AMber 9. In case of conformational change in the
receptor and ligand, it is recommended to use 3 species method. i.e to
run the MD with the ligand, receptor and complex solvated
individually. How can I extract the final snapshots and energies for
these 3 species?

The other question I have is why it is recommended to use delphi over
default PB-solver in Amber for charged ligands?

Many thanks! 

-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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