Re: [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap

From: David A Case <>
Date: Mon, 7 Jun 2021 07:46:50 -0400

On Mon, Jun 07, 2021, Dr. Anselm Horn wrote:

>Note, that ambpdb from the AmberTools has the flag '-offset' to allow
>for a shifting in residue numbering.

The ambpdb program also has a more general flag, '-ext', that uses residue
numbers and other information (occupancies, B-factors, etc.) from the
original PDB file. To use this, you need to first have used the addPdb
action in ParmEd to transfer this information from the PDB file to your
prmtop file.

The pdb4amber program creates a file that maps original residue numbers to
their internal (Amber) counterparts, which can be helpful for those writing
their own scripts.

[Aside: the origin of all those goes back to the 1980's, when the choice
was made to ignore chainId's in Amber codes. In multi-chain proteins, it
is only the residue number/chainId pair that is unique, and not just the
residue number itself. So, Amber creates a "residue index" (starting at
1 and incrementing for each new residue) but treats that like a "residue
number" in writing PDB files. I don't expect the code to change anytime
soon, but we should update the documentation to refer to the internal number
as an "index".]


p.s. OK,OK: it's actually the residue number/chainId/insertion code triplet
that needs to be unique....

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Received on Mon Jun 07 2021 - 05:00:02 PDT
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