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

From: Thomas Evangelidis <>
Date: Thu, 6 Dec 2018 11:09:31 +0100

Hi all,

Thank you for the explanation. It seems that at some point the TER records
were deleted while I was removing the ligand from the complex. But still
the last protein residue is 385 and all following atoms belong to waters
with resid starting from 501. tleap should be capable of recognizing the
C-term. After all, it does recognize it when it writes the intermediate pdb
file (protein1.pdb).


On Thu, 6 Dec 2018 at 03:25, David Case <> wrote:

> 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
> missing....)
> ....dac
> _______________________________________________
> AMBER mailing list

Dr Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <>
Prague, Czech Republic
CEITEC - Central European Institute of Technology <>
Brno, Czech Republic
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Received on Thu Dec 06 2018 - 02:30:01 PST
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