Re: [AMBER] Automated capping of missing loops?

From: David A Case <>
Date: Thu, 14 Oct 2021 21:19:23 -0400

On Thu, Oct 14, 2021, Brian Radak wrote:

>Is there a script in AmberTools that automates insertion of capping groups
>(e.g., ACE and NME) along with TER characters when prepping a PDB for
>tleap, etc.? I was kind of shocked when the manual suggested doing this by
>hand as the obvious way. Would this be an attractive feature in pdb4amber
>or are there simply enough third party preparation tools available on an
>academic license?

pdb4amber will tell you where the gaps are, but does not impose any particular
way to handle them. I've never used ACE/NME in this situation, but that is
just me. What phenix (and I) do with gaps is to use pdb4amber to find the
gaps, then just add a deleteBond command to the tleap script to remove the
bond that tleap creates during the loadPdb command. This leaves dangling
ends, but that is not an obvious problem for molecular mechanics force
fields. No need for TER cards in any pdb file, although they will appear if
you later use ambpdb with the final prmtop file as input.

Maybe others on the list have a more sophisiticated workflow here.


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Received on Thu Oct 14 2021 - 18:30:02 PDT
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