AMBER: RE: Restrain of dihedral angle!

From: Yong Duan <>
Date: Fri, 1 Aug 2003 09:27:04 -0400

You probably can try NMR option with large penalty terms. This should be
ok with energy minimization.


-----Original Message-----
From: Marco Aurelio Correia Preto [] On
Behalf Of Marco Aurelio Correia Preto
Sent: Friday, August 01, 2003 6:59 AM
Subject: Restrain of dihedral angle!

Dear Amber users:

We've been testing some parameters for non-coded amino acids!
One test we would want to perform is the comparison between the energy
profile of the MM calculated profile and an QM calculated profile!

I know Amber does not support any option to do this automatically, but I
was hopping we could restrict the dihedral to a fixed value, perform an
optimization on the hole unit and then (after frreiing the restriction)
perform a single point to have an MM energy read!

It would be necessary to do this to each point of the profile!

We've been trying to use restraintorsion unit a1 a2 a3 a4 999999999
danglevalue 1 in xleap to keep the dihedral on the disered value but we
are not achiving this objective.

Unless we are wrongly difining the atoms (we use
unit.residuenumber.atomname) we don't understand the obtained values! We
would expect a constrain en value of zero for the first point of the
optimization (because the starting geometry has the desired value), but
we don't.
Even worst is the fact that the restrain decreesses it's value when
moving away from the value difined by us!

We belive that the restrain is not being correctly aplyed by us.
Can anyone help us on this?

Sincerely yours

Marco Preto
Ph. D. student
FCUP - Porto

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Received on Fri Aug 01 2003 - 14:53:01 PDT
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