AMBER Archive (2007)

Subject: Re: AMBER: torsion angle

From: deepti nayar (deepti.icgeb_at_gmail.com)
Date: Thu Mar 15 2007 - 00:13:43 CST

hi

thank you for the cooperation. i am trying to use impose. but one
thing more i would like to ask that apply torsion restraint i will use
during MD but what if i have made a non standard residue in xleap and
now i want to fix some torsion angles. how can i do that? similarly,
for NEB MD, i have to make two conformations of my peptide (one of
whuich would serve as initial and the other would as final), how do i
have to set (fix) the torsion angle in this case?

please guide me through this.

thanks
deepti

On 3/14/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> you can try using "impose" in leap, or you can apply a
> torsion restraint during MD ("NMR restraints") and change
> the restraint position with time to force it to move to the desired angle.
>
> On 3/14/07, deepti nayar <deepti.icgeb_at_gmail.com> wrote:
> > hi amber users
> >
> > i am able to run addles now and so there is no problem with the NEB
> > tutorial. bt please tell me where can one change the torsion angle of
> > a peptide to make a protein with different conformation.
> >
> > thanx
> > deepti
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