Hi AMBER users -
I'm trying to fix the main chain of part of my protein during a
simmulated annealing by using ibelly, and selecting the part of the
structure that I *allow* to move in the group definition, as shown in
the manual. When I check the output, I notice that the main-chain atom
velocities are zero, as expected, but also that the *all* the atoms in N
and C terminal residue of the fragment allowed to move are "fixed" (i.e.
zero velocities). Any explanation for this strange behaviour?
I'm also having problems with defining the atoms correctly: if I want to
"freeze" the main chain atoms with ibelly, than I must specify in the
group selection the side-chain (i.e. that part of the structure allowed
to move); if I do this as in the example in the manual:
* * S *
* * B *
* * 3 *
* * E *
this wll allow the amino hydrogen and the carboxyl oxygen (both of type
E) to move. If I don't include atoms of type E then all these atoms -
whethter they are main chain or side chain will be fixed. Any way around
that?
Thanks in advance,
Joseph
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Joseph Nachman Department of Biochemistry
nachman_at_hera.med.utoronto.ca University of Toronto
Medical Sciences Building
tel: +1 416 978-5510 Toronto, Ontario M5S 1A8
fax: +1 416 978-8548 Canada
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Received on Thu Dec 21 2000 - 14:37:25 PST
