Hi Gustavo,
You can check the webpage. In short, I made a small script to do this conversion instead of using antechamber.
Pengfei
> On Mar 28, 2020, at 12:31 AM, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
>
> Thank you. Can you please tell me which are the relevant changes?
>
> The error in this thread was solved by using Antechamber 17.3.
>
> Thanks,
> --
> Gustavo Seabra
>
> -----Original Message-----
> From: Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>
> Sent: Friday, March 27, 2020 4:58 PM
> To: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org>>
> Subject: Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial
>
> 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><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 Thu Apr 09 2020 - 08:30:02 PDT
