Re: [AMBER] Using chirality restraints for modified residues

From: David A Case <>
Date: Thu, 28 Jun 2018 14:31:13 -0400

On Thu, Jun 28, 2018, Baptiste Legrand wrote:
> When I launched calculations on pseudopeptides incorporating non-natural
> residues, I had chirality issues. So I would try to fix it using the
> chirality restraints on my non-standard residues. I first modified the
> makeCHIR_RST file to incorporate these latter and to simply use the
> makeCHIR_RST command but it still ignore them.

There must be some reason for this. The usual debugging strategy is to
set LISTIN=POUT in your input file: this will give detailed information
about how each restraint is being processed at the first step. You can
make sure that what you prepared is being read and interpreted in the
way you intended.

The makeCHIR_RST script just simplifies the creation of restraints, but
they look exactly like ones that could be hand-generated. You could
copy and paste them insided your .dist file if you want. There is not
enough information in your email to tell why the chirality restraints
are being ignored, but there has to be rational reason.


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Received on Thu Jun 28 2018 - 12:00:02 PDT
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