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

From: Stefan Ivanov <>
Date: Tue, 27 Nov 2018 20:35:46 +0200 (EET)

In the example restraint below, how is a chirality inversion possible when two of the atoms involved are both hydrogens, which are equivalent, atom type-wise? I am left with the impression that the "chirality" restraints are simply improper torsions intended to keep the atoms concerned in a tetrahedral geometry, although I don't see a good reason why they would adopt a non-tetrahedral one without these restraints. Am I correct?

>-------- Оригинално писмо --------

>От: David A Case

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

>До: AMBER Mailing List

>Изпратено на: 27.11.2018 20:08

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;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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