I can't give you an exact input file, but the general idea would be to
apply a torsion restraint and slowly change the target value from the
initial one to the desired one. Go slowly (nanoseconds) or else it will
distort the structure too much. Even then you will need to be careful, and
it's not clear if the rest of the structure will eb able to adjust
properly. Look the the Amber tutorials for more examples of restraints.
On Fri, Feb 6, 2015 at 12:45 PM, Dhiraj Srivastava <dhirajks.gmail.com>
wrote:
> I want to lock my peptide in cis conformation and see its effect on
> conformation and dynamics. is there any way to do that? the structure is in
> trans conformation. How can I convert it to cis? I am thinking about fixing
> the peptide during the simulation. is that a good idea?
>
> Thanks
> Dhiraj
>
> On Fri, Feb 6, 2015 at 11:32 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Look into work by Donald Hamelberg, I think he may have done work in that
> > area.
> > On Feb 6, 2015 11:40 AM, "Dhiraj Srivastava" <dhirajks.gmail.com> wrote:
> >
> > > Hi
> > > did any one tried to do simulation on the effect of cis-trans
> > > isomerization on protein conformation and dynamics? like prolyl
> > isomerases
> > > catalysed the cis-trans isomerization.
> > >
> > > Thank you
> > > Dhiraj
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Received on Fri Feb 06 2015 - 10:30:03 PST
