Olá Justin, thank you for responding to my post. I had tried what you mentioned before. All I get is that the some atoms are missing (see error message in the link https://sites.google.com/site/fileti/ ). In fact, as I just want NH3+ (from LYS) and COO- (from ASP), the other atoms are not included in PDB file and this can give error. If I put everything into the same group ("1" for example) many of the atoms are deleted by pdb2gmx because they are duplicates.
In fact I still do not quite understand the logic of creating a PDB from the aminoacid residues. I've read some tips on the list but still I could not understand. That's it. If you have any suggestion, it will be very useful. Até mais eef _______________________________________ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br ------------------------------ > > Message: 2 > Date: Thu, 26 Aug 2010 09:32:06 -0300 > From: Eudes Fileti <fil...@ufabc.edu.br> > Subject: [gmx-users] Dipeptide generation problem > To: gmx-users@gromacs.org > Message-ID: > <aanlktikwxuc1g8fq=fqnpfixswadstspha=9qjptd...@mail.gmail.com> > Content-Type: text/plain; charset="windows-1252" > > Hello everybody, > I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue. > This dipeptide has a positively charged site (NH3+) and a negatively > charged > site (COO-). > My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to be > consistent > and produces error when I execute pdb2gmx. > > The link above presents the PDB and the error message from pdb2gmx > (which I have not found similar in the forum). > > Could someone give me a hand with that? > > Bests > eef > _______________________________________ > Eudes Eterno Fileti > Centro de Ciências Naturais e Humanas > Universidade Federal do ABC — CCNH > Av. dos Estados, 5001 > Santo André - SP - Brasil > CEP 09210-971 > +55.11.4996-0196 > http://fileti.ufabc.edu.br > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100826/0cfce19f/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 26 Aug 2010 08:36:24 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Dipeptide generation problem > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4c765fc8.4020...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > Eudes Fileti wrote: > > Hello everybody, > > I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM > residue. > > This dipeptide has a positively charged site (NH3+) and a negatively > > charged site (COO-). > > My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to > > be consistent > > and produces error when I execute pdb2gmx. > > > > The link above presents the PDB and the error message from pdb2gmx > > (which I have not found similar in the forum). > > > > Could someone give me a hand with that? > > > > Your .pdb file contains various broken residues (ASP, LYS) and > non-sequential > numbering (i.e., those broken residues are all numbered 1). Clean up the > .pdb > and try again. > > -Justin > > > Bests > > eef > > _______________________________________ > > Eudes Eterno Fileti > > Centro de Ciências Naturais e Humanas > > Universidade Federal do ABC — CCNH > > Av. dos Estados, 5001 > > Santo André - SP - Brasil > > CEP 09210-971 > > +55.11.4996-0196 > > http://fileti.ufabc.edu.br > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > >
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