Re: [AMBER] bash scripting for MD tasks

From: Anselm Horn <>
Date: Wed, 24 Sep 2014 14:45:11 +0200

I totally agree that my proposal is far from being perfect.

However, it should serve as an example for a potential solution of the
problem provided (number of CYX residue) with all the limitations in
mind (for many pdb file the fourth column actually holds the residue name).
However, there's of course a difference between a script for a
specialized task and a more general one.

And I further agree, that this is not an AMBER-related topic.



Am 24.09.2014 14:18, schrieb Hannes Loeffler:
> Ouch.
> Just a few problems I spotted with this:
> 1) grep ATOM: will return _any_ line with the string 'ATOM' occuring
> _anywhere_ on a line; some codes may also decide to use 'HETATM'
> instead because CYX is non-standard
> 2) grep CA: same as above, could be calcium atom, part of a residue
> name, segment name or possibly some other abuse of the format or simply
> any occurence on a non ATOM/HETATM record
> 3) awk: the ancient PDB format is a _fixed-column_ format which also
> implies that columns can "run" into each other while awk splits (by
> default) on whitespace which may not be there; also, the residue
> name is not the 4th datum in a ATOM/HETATM record.
> The two lines code doubles this but why would one need parse the input
> twice anyway?
> Cheers,
> Hannes.

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Received on Wed Sep 24 2014 - 06:00:04 PDT
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