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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jun 22 2008 - 06:07:05 PDT
