Dear Amber users!
I'd like to perform some test simulations using QM/MM method of
parametrization mainly based on that tutorial
https://mmtsb.org/workshops/mmtsb-ctbp_workshop_2009/Tutorials/qmmm_amber/index.htm
Firstly I have just simulated water-soluble protein-ligand system (this
time ligand have been parametrized by gaff) and would like to perform the
same simulation but changing treatment of my ligand to:
qmmask = ':200' # number of ligand residue
qmcharge = 1 # because my ligand hase total -1 charge
qm_theory = 'PM3'
as I noticed that simulation should be exactly like above mentioned example
shouldn't it? Should I re-parametrize my ligand for such case (E.g using
REDS)?
James
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Received on Mon May 12 2014 - 03:00:02 PDT
