Re: [AMBER] EstJ6_DBP_bound_sus

From: David Case <>
Date: Tue, 24 Sep 2019 11:55:54 +0000

On Tue, Sep 24, 2019, wrote:
>Warning: There is a bond of 5.004838 angstroms between:

cc-ing to Scott: he is the most likely person to know why tleap is
giving a message like this, but with blanks where the atom
identification is supposed to be. We may need to get a small example
file from you to try to reproduce the problem.

>FATAL: Atom .R<HIE 76>.A<HD1 18> does not have a type.

Amber by default assumes that histidines are HIE. But your input PDB
file has HD1 protons, which implies that the histidine should be either

In my previous email (did you ever see that?), I suggested running your
pdb file through pdb4amber. That should identify at least some gaps in
the structure (which might lead to long "bonds", and will fix the
histidine problems. You then feed the output pdb into tleap.

....hope this helps....dac

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Received on Tue Sep 24 2019 - 05:00:03 PDT
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