Re: [AMBER] two questions about Amber annealing

From: Ross Walker <>
Date: Sat, 19 Jun 2010 21:55:47 -0700

Hi Yiyu,

> I am a new user of Amber. I met two problems when using Amber 10 sander
> for protein annealing (0K-1200K-0K) with some distance and angle
> constraints.
> (1) I often met following problem:
> "Coordinate resetting (SHAKE) cannot be accomplished, deviation
> is too large
> Note: This is usually a symptom of some deeper problem with the
> energetics of the system."

A 1200K you are probably seeing issues with the integration, plus the fact
your protein is almost certainly unstable at this temperature. Do you have a
specific reason for needing to go this high? Realize at 1200K in reality you
would be boiling all the water off and your protein would probably be
decomposing. In the simulation at the very least it is probably completely
unfolding. You can probably use a shorter time step to get the simulation
stable, 1fs with shake will probably work but you may need to go to 0.5fs or
so to be sure.
> (2) I got some cis-peptides when I use annealing-minimization to refine
> my protein structures. I know one solution is to put the omega=180
> constrains to the peptide bonds for annealing. May I know whether there
> are another solutions? Or are there any programs can fix the geometry
> problems of a protein structures?

Is this really happening during minimization? This seems very unlikely. If
you mean during heating to 1200K then that seems perfectly reasonable. The
cis-trans barrier is probably crossable around 350K or so, so 1200K will
almost certainly cause such changes. You can add restraints to stop it but
ideally you probably want to rethink your annealing protocol.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Sat Jun 19 2010 - 22:00:02 PDT
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