Re: [AMBER] Ligand show error in Dock complex

From: David A Case <>
Date: Thu, 4 Jul 2013 08:58:04 -0400

On Thu, Jul 04, 2013, wrote:

> Created a new atom named: HD1 within residue: .R<HIE 249>
> Created a new atom named: HD1 within residue: .R<HIE 573>

Your pdb file has HD1 atoms on histidine, but the default histidine in Amber
is HIE, with no HD1 atom. You need to change the the residue name in the PDB
file to either HIP or HID, depending on which atoms are in the PDB file.

[Some developer should fix this problem: Leap should check histidines for
inconsistent hydrogen placement and do the right thing.]

> Created a new UNIT for residue: UNK sequence: 649

Your pdb file has a residue named UNK, but LEaP doesn't have any units loaded
named UNK. You can use the "list" command in LEaP to find out what units
it knows about. You will have to edit the pdb file to change the UNK (=
"unkown"?) residue to the name in the correct LEaP unit.

...good luck...dac

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Received on Thu Jul 04 2013 - 06:00:01 PDT
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