Re: [AMBER] Atom Expression in NAB

From: case <>
Date: Sun, 8 Dec 2013 11:29:57 -0500

On Sun, Dec 08, 2013, sunita gupta wrote:

> I have a protein-lignad complex (231 residues protein and 232nd residue as
> ligand). While setting up MD for this complex I want to fix the protein,
> and if I am selecting ':1-231' as restrainmask, it is selecting the ligand
> as well.

NAB atom expressions are different than those in the rest of Amber: they
have three sections (chain (aka strand, aka molecule), residue, atom), and
the residue numbers start over at 1 for each new chain.

Hence, you atom expression selects residues numbered 1-231 in each chain: this
will include the ligand (which is presumably the first residue in the second
chain.) What you probably want is "1::" (for the entire first molecule).

...good luck...dac

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Received on Sun Dec 08 2013 - 09:00:02 PST
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