Harmonic restraints for moving residue positions??

From: Charles Danko (dankoc_at_gmail.com)
Date: Sat Jan 08 2005 - 15:03:50 CST


I am trying to move the N and C terminus tails to positions that they
are likely to take such that I can dock models of two domains. Since
I can calculate approximately where this point is going to be, I was
thinking of using harmonic restraints to move the tails of both
proteins into their approximate position. Does anyone see any
problems with this approach?

Should the values listed in a previous thread of consexp =2 and the
force constant = 5 be adequate to work in this situation?? If I
decide to go with a higher force constant, do you advise that I ramp
up to this higher number? And finally, should I apply force to only
one atom (e.g. the backbone N, or backbone C for moving N and C
respectively), or do you recommend applying forces to the entire

Many thanks for all answers/ suggestions.

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