Re: [AMBER] valiine chirality inversion

From: David Case <>
Date: Sat, 21 Jan 2017 22:09:18 -0500

On Thu, Jan 19, 2017, Thomas Pochapsky wrote:

> Hi, I found that two valines in my structure (the result of solvated
> RDC-restrained dynamics w/ AMBER 14), have inverted chirality; checking
> the AMBER archives, I see that this can happen when a crystal structure
> is protonated by Leap during hydrogen builds and subsequent minimization.

I'm betting that your problem has nothing to do with Leap, but you can check
by looking at the chiralities right after the Leap step. More likely is that
strong NMR restraint forces during dynamics can lead to chirality flips.

Look at the makeCHIR_RST script in $AMBERHOME/bin: that will allow you to add
chirality restaints to your protein to prevent chirality flips.


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Received on Sat Jan 21 2017 - 19:30:03 PST
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