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.scripps.edu on behalf of Elijah Gregory
Sent: Tue 10/24/2006 6:17 PM
To: amber.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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Received on Sun Oct 29 2006 - 06:07:09 PST
