Thanks, Marc!
Question regarding intal system preparation: for instance I have pdb
consisted of GFP with chromophore and I'd like to perform qm_mm simulation
of this protein treating chromophore by semi-empirical approximation and
rest of the protein (+ solvent) using mm. How I should prepare initial
prmtop of my GFP using tleap if I lack for the parameters for chromophore
(wich are actualy will not be usefull during my qm-mm run) ?
James
2014-05-13 18:06 GMT+04:00 Marc van der Kamp <marcvanderkamp.gmail.com>:
> Hi,
> You should certainly define the qm_mm mask with atom subsets. Check out the
> ambermask syntax.
> You will need to determine which part of the chromophore you require to be
> QM. If it is the whole chromophore, you have no choice but to put
> link-atoms in the peptide-backbone. This is not ideal, but can be ok. I
> would say that the best place is between C and CA atoms (so you'll end up
> treating a little bit of the backbone QM as well). Best not to put a link
> atom between C and N, as this is a more polarized bond.
> --Marc
>
>
> On 13 May 2014 14:09, James Starlight <jmsstarlight.gmail.com> wrote:
>
> > Thanks Marc!
> >
> > Regarding bonds between atoms treated in qm and mm approximations: will
> it
> > be more correctly to define qm_mm mask using some atom subsets (not
> > entirely residue number)- e.g excluding atoms which are connected to the
> > rest of the protein backbone. E.g having GFP chromophore which is
> > covalently attached to the rest of the protein backbone both from its N
> and
> > C termi- it would be logically to define connectors as chromophore's N
> > (connected to the previous C atom of the adjacent amino acid) and C
> > (connected to the N atom of the next a.a) atoms. So It seems that all
> > chromophore atoms should be defining in the qm'mm mask besides its first
> C
> > and last N atoms, shouldn't it? How it could be defined in amber input
> > file?
> > If I misunderstood It I's not well clear for me what connectors in the
> case
> > of GFP chromophore might be placed automatically if I just define
> > :name_of_Chromophore_residue as the qmmm mask.
> >
> >
> >
> >
> >
> > James
> >
> >
> > 2014-05-13 16:42 GMT+04:00 Marc van der Kamp <marcvanderkamp.gmail.com>:
> >
> > > 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 Wed May 14 2014 - 02:00:02 PDT
