Re: [AMBER] tleap does not add OXT when I load a crystal structure

From: David Case <>
Date: Thu, 6 Dec 2018 02:22:26 +0000

On Thu, Dec 06, 2018, Thomas Evangelidis wrote:
>I am curious why when I load a pdb of crystal structure without hydrogens,
>tleap does not add OXT at the C-terminus.

As Dave pointed out, you definitely need a TER card after the protein
chain, and before the first water moleule. Where did "receptor.pdb"
come from? I don't recall seeing this problem with a "real" PDB file
(e.g. from

(Aside: note that the receptor.pdb file itself has no OXT atom, and
there is no change in chain ID on going from protein to waters. So all
the usual hints that one has reached a C-terminal residue are


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Received on Wed Dec 05 2018 - 18:30:03 PST
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