Custom Search
-- Gustavo Seabra -----Original Message----- From: Pengfei Li <ambermailpengfei.gmail.com> Sent: Friday, March 27, 2020 4:58 PM To: AMBER Mailing List <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>. 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 >>> >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Mar 27 2020 - 22:00:02 PDT