AMBER: Simulating a section of a molecule

From: Dave, Sonya <>
Date: Thu, 15 Feb 2007 10:59:53 -0600

I am trying to make a 3D structure of an alpha helix, which is part of a larger molecule. I'm doing it using homology modeling and refining use Molecular Dynamics. This isn't really an amber question, as much as maybe something from your experience.
My "alpha helix ", when simulated, doesn't look like an alpha helix at it's ends. The middle amino acids do resemble a helix though (it's 7 a.a. total). I believe, in the true structure, the whole thing is a helix. Do you think this "improper" structure could be because I don't have the whole molecule? Perhaps, because the end amino acids don't have neighboring amino acids, They may not show proper secondary structure. I'm using explicit solvent. Each simulation takes quite a while, so I just wanted your opinion about whether I should try rerunning the simulation with more amino acids on each side of the helix to fix the structure. But, perhaps the problem is something completely different (like i'm not using a proper force field).
Another question is, would you consider something to be a alpha helix/beta sheet, etc, even if programs (VMD, Chimera, DSSP, etc) don't call it one. Do you treat what the programs tell you as secondary structures as strictly correct?
I know this isn't exactly an amber question. However, I don't have much experience with simulations, or structural biology in general, and don't yet have ready access to people who can help me on campus. But I appreciate your help on the issue.

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Received on Sun Feb 18 2007 - 06:07:20 PST
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