[gmx-users] Dipeptide generation problem [Justin]

[Eudes Fileti]

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 <fileti at ufabc.edu.br>
> Subject: [gmx-users] Dipeptide generation problem
> To: gmx-users at gromacs.org
> Message-ID:
>        <AANLkTikWxuC1g8fQ=fqnPfiXSWaDSTsPha=9QjPTDY38 at 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
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> ------------------------------
>
> Message: 3
> Date: Thu, 26 Aug 2010 08:36:24 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Dipeptide generation problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4C765FC8.4020306 at 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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