Some additional questions:
1) Does it possible to use *.prmtop and *.inpcrd files made from the
previous equilibration MD run For instance initially my ligand was
parametrized by force field method and its parameters have been included in
the prmtop which I'd like to use as the input for qm_mm defining ligand
treatment by ab initio? Will force field parameters of this group be
ignored during qmmm?
2) How should I made *.prmtop file if I'd like to run qmmm calculations
with the ab initio treatment of one of the non-standart residue which is
covalently connected to the rest of the protein backbone (e.g as in
Rhodopsin or GFP). Should I define that covalently bonds with the rest of
the protein backbone explicitly in the conf file ?
3)Again I'll be very thankful for some tutorial covered that questions as
well as some theory background of the ab initio methods implemented in the
amber.
James
2014-05-13 15:39 GMT+04:00 Marc van der Kamp <marcvanderkamp.gmail.com>:
> 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
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> > >
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> >
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Received on Tue May 13 2014 - 05:30:03 PDT
