Some additional answers ;)
On 13 May 2014 13:02, James Starlight <jmsstarlight.gmail.com> wrote:
> 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?
>
> Yes. You can use the same *.prmtop and *.inpcrd (or *.rst or whatever).
Just select the ligand in the qmmask in the qmmm section of the inputfile.
Force field parameters will be ignored for all atoms treated QM.
>
> 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 ?
>
In the same way as a non-covalent residue, BUT you will want to think about
which atoms should be treated QM and which MM - Amber will automatically
place link-atoms to treat the covalent QM/MM boundary. Best is to pick
non-polar bonds (like CA-CB in amino-acid side-chains) as the qm/mm
boundary.
> 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.
>
> Others may know of tutorials (outside those on the amber website).
There are no 'ab initio' methods inplemented in AMBER, 'only' a range of
semi-empirical methods (see sqm in AmberTools manuals).
You can interface with QM programs to use other methods.
"some theory background" is a bit too vague here - there are numerous
textbooks that can help you, but a thorough understanding of the enormous
range of existing QM methods (that could be roughly characterised as
semi-empirical, DFT, or ab initio) will take years of study...
> James
>
> --Marc
>
> 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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Received on Tue May 13 2014 - 06:00:02 PDT
