From: Valeria Losasso (losasso_at_sissa.it)
Date: Wed Jul 02 2008 - 03:38:20 CDT
Hi all,
my question is the following: in my protein I have three long interacting
alpha helices. First of all I minimized the side chains by blocking the
backbone through a constant force. Nevertheless, if I try to minimize the
entire protein (since the previous step is clearly not enough to start a
dynamics) I get a series of distortions in the backbone of the helices,
probably due to their length and position.
The point is: is there an "automated" way to keep the secondary structure
with the correct parameters (dihedral angles and so on) - I mean: a way to
say "I want a standard alpha helix from residue X to residue Y"?
Or I have to setup
manually all needed restraints among all atoms involved? And in this
second case, is it more
convenient to restraint the hydrogen bonds length or dihedral values or
what?
Best regards,
Valeria Losasso
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