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 - 07:30:02 PDT
