Hi Gustavo,
I have made a relevant update in the tutorial: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
You can do a try to see whether it works.
Pengfei
> On Feb 27, 2020, at 9:10 AM, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
>
> Thanks a lot David and Marcelo,
>
> Using '-dr n' or '-dr no' didn't help, and I still got the same error.
> However, rolling back to Antechamber 17.3 works nicely:
>
> $ antechamber -fi pdb -fo mol2 -i ZN.pdb -o ZN_pre.mol2 -at amber -pf y
> Welcome to antechamber 17.3: molecular input file processor.
> acdoctor mode is on: check and diagnosis problems in the input file.
> -- Check Format for pdb File --
> Status: pass
> -- Check Unusual Elements --
> Warning: Unusual element () for atom (ID: 1, Name: ZN).
> GAFF does not have sufficient parameters for molecules having unusual
> elements (those other than H,C,N,O,S,P and halogens).
> To ensure antechamber works properly, one may need to designate
> bond types for bonds involved with unusual elements.
> To do so, simply freeze the bond types by appending "F" or "f"
> to the corresponding bond types in ac or mol2 files.
> -- Check Open Valences --
> Warning: This molecule has no hydrogens nor halogens.
> It is quite possible that there are unfilled valences.
> -- Check Geometry --
> for those bonded
> for those not bonded
> Status: pass
> -- Check Weird Bonds --
> Status: pass
> -- Check Number of Units --
> Status: pass
> acdoctor mode has completed checking the input file.
>
>
> It really seems to be a bug introduced in some later version of
> Antechamber.
>
> All the best,
> --
> Gustavo Seabra.
>
>
> On Thu, Feb 27, 2020 at 3:50 AM Marcelo Andrade Chagas <
> andrade.mchagas.gmail.com> wrote:
>
>> Dear Gustavo Seabra.
>>
>> In the AMBER16 version it works normally when using antechamber.
>>
>> There's nothing wrong with Zn.pdb input file.
>>
>> I suggest using AMBER16 version, if possible, for the parameterization
>> process when reproducing this tutorial,
>> or check the problem in the version used.
>>
>> Best regards.
>>
>> Marcelo
>>
>> Dr. Marcelo Andrade Chagas,
>> http://lattes.cnpq.br/7024808363863350
>> *eCsMo**Lab**: Laboratório de Estudos Computacionais em Sistemas
>> Moleculares*
>> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
>> * http://lqcmm.qui.ufmg.br/
>>
>> Departamento de Química, ICEx, Universidade Federal de Minas Gerais
>>
>> 31270-901, Pampulha, Belo Horizonte, MG, Brazil.
>> Tel:(31)3409-5776
>>
>>
>> David A Case <david.case.rutgers.edu> escreveu no dia quarta, 26/02/2020
>> à(s) 23:19:
>>
>>> On Wed, Feb 26, 2020, Gustavo Seabra wrote:
>>>>
>>>> I'm having a weird error with Antechamber here,
>>>
>>> update to the last email: it might be "-dr n" instead of "-dr no".
>>>
>>> ...dac
>>>
>>>
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Received on Fri Mar 27 2020 - 14:00:02 PDT
