[gmx-users] conveniently placing restraints on a subset of a molecule

[Justin Lemkul]

On 12/28/19 12:41 PM, Miro Astore wrote:
> Hello,
>
> I am new to the gromacs work flow, I come from using NAMD.
>
> An example of what I want to do is place harmonic restraints on a subset of
> a molecule, for example all of the CA atoms in a protein backbone. I have
> found the genrestr function which I would have expected would do the trick.
>
> However, as stated in the documentation the indexes won't reflect those
> within the molecule. I'm wondering if there is a simple way to do what I
> want using the gromacs work flow that doesn't include manually editing the
> itp files.

Restraints are a topology construct and are therefore only valid from 
1..N for a given molecule of N atoms. Global atom indices are indeed 
invalid. genrestr will produce a correct restraint topology for the 
first molecule in a coordinate file (e.g. starting from atom number 1), 
but you can supply the program any coordinate file that is numbered from 
1. If you have multiple proteins, extract the coordinates of the protein 
of interest, renumber it with editconf, and supply that file to genrestr.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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