AMBER Archive (2008)

Subject: AMBER: Conformation search...

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Thu Apr 17 2008 - 14:32:52 CDT

Hi User:
We have a protein with two domains. This two domains were connected by two
linkers of different length. We want to study the different conformation that
the protein domains can adopt depending the length of the linkers without
loosing the secondary structure feature present. I was thinking in use some
position restrain in the backbone atoms of the domains and leave the linkers
and all the side chains to move freely but this aproach will not let the
system to change the conformation.
With a dihedral constraint it will be posible to do what I want to do?
How can I do it?
There is any other option to do this?

Best Regards,
Anthony
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