Yes, that is what it means. QM/MM can only be run with sander.
--Marc
On 13 May 2014 12:34, James Starlight <jmsstarlight.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue May 13 2014 - 05:00:06 PDT
