Re: [AMBER] Automated capping of missing loops?

From: David A Case <>
Date: Mon, 18 Oct 2021 15:44:38 -0500

On Mon, Oct 18, 2021, Brian Radak wrote:

>The gaps are large enough that I don't want to naively guess the
>coordinates but do not want artificial charge - that's it.

If you just let tleap create the system, then remove the bond that is
across the "gap" (either in your tleap script itself, or later via ParmEd),
it should get what you describe above: you are not "guessing" about any
coordinates that are not in the original PDB file, and there are no
artificial charges. (This assumes that the "gap" consists of a set of
contiguous residues that are completely missing.)

[Note that the workflow above is *not* the same as putting a TER card into
the input PDB file; the latter would be, by default, setting charged ends
before and after the gap.]


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Received on Mon Oct 18 2021 - 14:00:02 PDT
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