Hi,
Check your residue name:
Your residue name has to match the protonation state of your HIS. Leap automatically chooses HIE for all HIS-named residues. Your need to choose HID or HIE for each residue.
1) In your PDB file, rename residues to HID if you want your protonation state to be HID on all those residues.
OR
2) Delete your HD1 atom in all your residues if you want an HIE protonation state. HIE residue name doesn’t contain an atom called HD1. So leap is confused.
Maria
> On Feb 25, 2022, at 8:46 PM, Sadaf Rani <sadafrani6.gmail.com> wrote:
>
> Dear Amber users
> I am using a pdb structure of protein. During leap processing I get the
> following error message:-
> Loading PDB file: ./protein_noH.pdb
> Created a new atom named: HD1 within residue: .R<HIE 32>
> Created a new atom named: HD1 within residue: .R<HIE 155>
> Created a new atom named: HD1 within residue: .R<HIE 263>
> Created a new atom named: HD1 within residue: .R<HIE 451>
> Created a new atom named: HC within residue: .R<CHIE 513>
> Added missing heavy atom: .R<CHIE 513>.A<OXT 18>
> total atoms in file: 7834
> Could you please suggest how I should correct the above-mentioned problem?
> I want to keep the protonation state of histidine the same.
> I have also tried with pdb4amber but still the same error.
> Thanks in advance for your help.
> Regards
> Sadaf
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Received on Sat Feb 26 2022 - 05:30:02 PST
