AMBER Archive (2006)

Subject: AMBER: How do we simulate deletion mutations

From: Dave, Sonya (sonya.dave_at_vanderbilt.edu)
Date: Wed Oct 25 2006 - 13:47:38 CDT


Hello,
 
I have a protein segment which is about 70 a.a. I have the crystal stucture model. In amber, is there a way to simulate the effect of deleting 17 of those amino acids(the 17 are continuous)? If not amber, are there any other programs that will do it? How would I approach this?
 
I also want to get simulate the effect of deleting those amino acids in a simulated (not crystal stucture) version of a similar protein segment.
 
Thanks,
Sonya Dave'

________________________________

From: owner-amber_at_scripps.edu on behalf of Elijah Gregory
Sent: Tue 10/24/2006 6:17 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Not getting proper structure after minimization

As far as parameter sets.... you should know that most forcefields out
there overemphasize alpha-helix structure.... it's trickier to
simulate alpha/beta structures. Look in the literature for *anything*
done with MD and your protein (or related homologues) for more hints
and tricks. MD is not easy, but nothing ever is =P

~Elijah
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