Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Thu, 27 Feb 2020 09:10:03 -0500

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 Feb 27 2020 - 06:30:02 PST