Re: [AMBER] Problems of pdb file convertion by pdb4amber and mmtsb

From: David A Case <>
Date: Mon, 10 Nov 2014 07:12:02 -0500

On Mon, Nov 10, 2014, LI An-Bang wrote:
> I used pdb4amber to convert some pdb files, and I found there maybe some
> problems of pdb4amber in converting pdb files.

There are lots of tools, including many in amber, that don't correctly deal
with insertion codes. Note that Amber re-numbers residues from 1 to N (with
no insertions) at the end anyway.

It sounds like pdb4amber is doing what Amber needs it to do.

There is some support in the add_xray program for handling these sorts of
issues, but genuine "support" won't be available until the next release. And
full "support" is a long way off: lots of things like atom masks rely on
having residue identifiers be just numbers.


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Received on Mon Nov 10 2014 - 04:30:02 PST
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