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 - 07:00:02 PDT
