AMBER Archive (2007)

Subject: Re: AMBER: phe-phe simulation

From: deepti nayar (deepti.icgeb_at_gmail.com)
Date: Wed Mar 28 2007 - 05:28:51 CST

thank yoi. I will try it and let you know.

On 3/27/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> 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_at_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_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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