AMBER Archive (2007)

Subject: Re: AMBER: phe-phe simulation

From: deepti nayar (deepti.icgeb_at_gmail.com)
Date: Tue Mar 27 2007 - 06:48:01 CST

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_at_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_at_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_at_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
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