Re: [AMBER] Equilibration

From: Bill Ross <>
Date: Wed, 22 Nov 2017 22:39:42 -0800

Dear Sara,

I am not the best expert here, since I have never modeled a protein, but
modulo that, it seems like a reorientation of the dangling 19 residues
would not be such a big deal. It would help to see the model with both
orientations showing, to see what the difference is, since it appears
like it is a stable mode shift vs. just flapping around.

Hopefully someone with more applied experience will chime in.


On 11/22/17 10:30 PM, wrote:
> Dear Bill,
> I checked the RMS fittings and observed that there was a prominent
> fluctuation in the RMSD of the terminal residues (19 residues). I have
> attached images of the protein showing the terminal residue and the RMSD
> fluctuation. Shall i continue with the production or do I have to
> cap/remove the terminal and start over.
> Best REgards,
> Sara
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Received on Wed Nov 22 2017 - 23:00:04 PST
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