On Mon, 2014-05-12 at 13:32 +0400, James Starlight wrote:
> 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
Then your qmcharge should be -1, not 1.
> 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)?
Parameters for a ligand you plan on treating with QM in a QM/MM
simulation are ignored. Residues are modeled with _either_ the force
field parameters _or_ the semiempirical QM Hamiltonian, not both.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 12 2014 - 04:30:03 PDT
