Dear all,
I am trying to rebuild the alpha helix of one the chains
which got destroyed during the simulation. I found that we can do that
by distance restraints. So my question what is a better way of
distance restraints i.e should I restrain the hydrogen bonds of the
helix or any particular bond distances. I was not clear when I read
the chapter 4 in manual, what type' should I use for this, are these
parameterized anywhere because the manual says type' should be 1 for
bonds but for hydrogen bonds it varies from 0-2. I found an exercise
by David van der Spoel
http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2004/exercises/index_html
but could not access the files, so I was not clear what atoms did he
use for restraints.
Thank you
abhigna
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