I would suggest doing the simulation without restraints first and making sure
that you see a problem before you try to fix it. I think it will be
fine. In fact
the rings are not supposed to be perfectly planar all the time, they
do bend somewhat.
I don't know anything about sybyl and its protein force field so I
don't know if those
have a problem.
On 3/27/07, deepti nayar <deepti.icgeb.gmail.com> wrote:
> I have 2 phenyl rings in my molecule and i want both of them to move
> during the simulation . In SYBYL ,when I do the simulation, I could
> see the rings puckering and so I am afraid that this might be the case
> here also.
> I want to ensure that this doesnt happen.
>
>
>
> On 3/27/07, deepti nayar <deepti.icgeb.gmail.com> wrote:
> > hi, by fixing the rings i mean that i dont want them ti move. i want
> > to restrain their movement. let them be in the plane where they
> > currently are.
> >
> > On 3/26/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> > > you need to tell us more. what do you mean by "fix" the rings,
> > > and why do you think it would pucker them?
> > >
> > > On 3/26/07, deepti nayar <deepti.icgeb.gmail.com> wrote:
> > > > hi
> > > >
> > > > I am carrying out phe-phe simulation and I have to fix the phenyl
> > > > rings. I fear whether it would cause puckering of phenyl ring thus
> > > > giving rise to unnecesary high amount of energy? any sugguestions
> > > > would be greatly appreciated.
> > > >
> > > > thanks
> > > > deepti
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Mar 28 2007 - 06:07:40 PDT
