On Sun, Jun 11, 2017, Mustafa Alhaji Isa wrote:
> I want to create topology and coordinate files of protein-ligand
> complex. but when I load the complex it display the below commands and
> subsequently failed the create the files
>
> Created a new atom named: HD2 within residue: .R<ASP 80>
> Created a new atom named: HD1 within residue: .R<HIE 137>
> Created a new atom named: HD1 within residue: .R<HIE 193>
> Created a new atom named: HD1 within residue: .R<HIE 408>
> Created a new atom named: HD1 within residue: .R<HIE 410>
To add to Bill's comments: you have hydrogen atoms in the PDB file that are
not in the libraries for these residue. If you have a protonated ASP, you
should change the residue name to ASH in the pdb file. If you have a HD1
atom in histidine, you either have HID (if the residue is neutral) or
HIP (if the residue is charged.)
...hope this helps....dac
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Received on Sun Jun 11 2017 - 05:30:03 PDT
