Thanks Jason!
Trying to launch such simulation on GPU usng pmed I've obtained
| ERROR: ifqnt must == 0!
| PMEMD 14 does not support QM/MM calculations.
| Please use sander 14 instead.
Input errors occurred. Terminating execution.
does it mean that qm_mm calculations could not be run on GPU?
James
2014-05-12 15:13 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> 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 Tue May 13 2014 - 05:00:04 PDT
