Re: [AMBER] how to stop making terminal residue

From: David A Case <>
Date: Tue, 11 Jan 2022 11:06:20 -0500

On Tue, Jan 11, 2022, Daniel Konstantinovsky wrote:

>Sure! Here is the pdb (below). The first DA is the one that tleap insists
>should be a terminal DA5, but is really a regular DA that will be connected
>to the STE residue via a tleap bond.

At the time of loading the pdb, tleap has no way to know that the first DA
residue is not a terminal one.

Here's how to fix that: after you source your leaprc files, add the
following lines to the tleap script:

addPdbResMap {
   { 0 "DA" "DA" }

This tells tleap to treat a 5' terminal ("0") DA as DA, over-riding (I hope)
the instructions in leaprc.DNA.xxxx to treat it as DA5.

Untested, but I think the idea is fine. You could also make a copy of
your leaprc.DNA.xxxx file and edit the addPdbResMap lines in that.


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Received on Tue Jan 11 2022 - 08:30:03 PST
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