Re: [AMBER] Why does makeCHIR_RST create restraints for side chains?

From: David A Case <>
Date: Tue, 27 Nov 2018 13:08:38 -0500

On Tue, Nov 27, 2018, Stefan Ivanov wrote:

> I am running replica exchange simulations of a protein and so I used
>makeCHIR_RST to create restraints for the backbone peptide groups. However, in the output from
>makeCHIR_RST I see that it is also creating restraints for the side chains. For example, for residue 1 (methionine in this case), I see
> # #
> chirality for residue 1 atoms:
>&amp;rst iat=5,10,8,9,

Feel free to modify the list of restraints that makeCHIR_RST creates to
suit your needs. It's "just" a shell script, and be sure to read the
comments at the top of the file.

Basically, the original goal was to create chirality restraints for all
tetrahedral carbons. If you just want restraints on the backbone, edit
the "chiral_defs" section of the script to remove the side-chains.
[It's not clear to me why one would wish to allow chiral inversions on
the side chains, however.]

> Also, what are trans-omega constraints and why are they also being created?

A "trans-omega" restraint keeps the omega peptide angle in the trans
region. As the capitalized warning in the script notes, you certainly
won't want to do this if you have a cis-peptide bond.

As with the similar makeXXXX_RST scripts, these are intended to be a
convenience to users. Feel free to modify them according to the needs
of your particular situation. (All of these scripts long precede the
invention of replica exchange simulations, for example.)


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Received on Tue Nov 27 2018 - 10:30:03 PST
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