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 - 07:30:04 PDT
