OK, but you can't 'predict' a transition state with MM only, as your atoms
(vdW spheres) will start overlapping well before you get to that, and your
MM energies are thus not going to be a reliable estimate of the 'real'
energy difference. So my comments still apply. Also, you will need to think
carefully about the reaction mechanism - there may well be more than just
one bond formation (perhaps a proton transfer as well?). This obviously
depends on the exact chemical reaction you're interested in.
Just trying out the restraint in MM (when the distance is still reasonably
large) is of course not a bad idea.
--Marc
On 18 September 2014 15:24, John Smith <ddfd09.gmail.com> wrote:
> I am actually trying to simulate the formation of the bond. My system is a
> docking complex in which the ligand just sits in the active site and I am
> planning to use QMMM to simulate the formation of the bond. Before that I
> want to construct a reaction path and predict the transition state. For
> that I am restraining the distances. I am planning to ass the QMMM terms to
> the input file once I succeed with the restraining
>
> On 18 September 2014 15:09, Marc van der Kamp <marcvanderkamp.gmail.com>
> wrote:
>
> > On a different note: you say you have a system with "an enzyme ligand
> > complex in
> > which the ligand binds covalently to a residue in the protein". If you
> want
> > to break a covalent bond (and that bond is defined by an MM bond term),
> > you'll have to use QM/MM (or other advanced techniques, such as EVB) to
> > actually 'break' the bond, otherwise you are just 'fighting against' the
> > harmonic bond term and the energy will simply go up very sharply.
> > Your current input doesn't specify anything but normal MM.
> >
> > --Marc
> >
> > On 18 September 2014 14:33, John Smith <ddfd09.gmail.com> wrote:
> >
> > > Thanks for the reply
> > >
> > > I added the LISTIN and what I am getting is "No restraint defined". How
> > can
> > > go around this?
> > >
> > >
> > > On 18 September 2014 13:19, David A Case <case.biomaps.rutgers.edu>
> > wrote:
> > >
> > > > On Thu, Sep 18, 2014, John Smith wrote:
> > > > >
> > > > > I am trying to construct an adiabatic map for an enzyme ligand
> > complex
> > > in
> > > > > which the ligand binds covalently to a residue in the protein. I am
> > > > > restraining a distance between a ligand atom and a protein atom
> over
> > a
> > > > > range. My input file for minimization looks like this
> > > > >
> > > > > #
> > > > > # 123 CYM SG 432 UNK C38 1.0 5.3 &rst
> > > > > ixpk= 0, nxpk= 0, iat=1937,6833, r1= 0.50, r2= 1.00, r3= 5.30,
> r4=
> > > > 5.80,
> > > > > rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
> > > > > &end
> > > > >
> > > > > When I run the minimization I only get zero values for the restrain
> > > like
> > > > > this:
> > > >
> > > > You should expect a zero restraint energy whenever the distance is
> > > between
> > > > r2 and r3 (i.e. between 1.0 and 5.3). I'm guessing that this is the
> > case
> > > > for
> > > > your initial structure.
> > > >
> > > > You can debug restraints (seeing detailed information about what is
> > being
> > > > calculated) by adding a "LISTIN=POUT" card right before or after that
> > > > "DISANG"
> > > > card.
> > > >
> > > > ...good luck....dac
> > > >
> > > >
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Received on Thu Sep 18 2014 - 09:30:03 PDT
