The error which you reported relating to HZ2 and HZ3 has something to do with the TYR atoms in you input file.
I have not had a chance to investigate this further, hopefully someone with experience of MCPB.py can chime in.
Best regards
// Gustaf
> On 8 Jun 2021, at 15:16, sabrine kh <sabrine.khelifa.gmail.com> wrote:
>
> On Mon, Jun 7, 2021 at 5:40 PM sabrine kh <sabrine.khelifa.gmail.com> wrote:
>
>> Hello sir,
>> Herein the input file
>> Thank you
>>
>> On Mon, Jun 7, 2021 at 2:27 PM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>>> You will most likely get a better response from someone who has
>>> experience using MCPB, however it seems that “HZ3” would be a hydrogen atom
>>> label?
>>>
>>> A quick guess would be that either it is located in an “bad” place or is
>>> not implemented for use with MCPB.
>>>
>>> Just based on these guesses, do you have a HZ3 atom in your input PDB
>>> file? Is everything lined up properly in the input structure file?
>>>
>>> Best regards
>>> // Gustaf
>>>
>>>
>>> On 7 Jun 2021, at 14:03, sabrine kh <sabrine.khelifa.gmail.com<mailto:
>>> sabrine.khelifa.gmail.com>> wrote:
>>>
>>> HZ3
>>>
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>>
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Received on Tue Jun 08 2021 - 07:00:02 PDT
