<div>Olá Justin, </div><div>thank you for responding to my post. I had tried what you mentioned before. </div><div>All I get is that the some atoms are missing (see error message in the </div><div>link <a href="https://sites.google.com/site/fileti/">https://sites.google.com/site/fileti/</a> ).</div>
<div>In fact, as I just want NH3+ (from LYS) and COO- (from ASP), the other atoms are not included </div><div>in PDB file and this can give error. If I put everything into the same group ("1" for example) many </div>
<div>of the atoms are deleted by pdb2gmx because they are duplicates.</div><div><br></div><div>In fact I still do not quite understand the logic of creating a PDB from the aminoacid residues. </div><div>I've read some tips on the list but still I could not understand.</div>
<div><br></div><div>That's it. If you have any suggestion, it will be very useful.</div><div><br></div><div>Até mais</div><div>eef</div>_______________________________________<br>Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>
Universidade Federal do ABC — CCNH<br>Av. dos Estados, 5001<br>Santo André - SP - Brasil<br>CEP 09210-971<br>+55.11.4996-0196<br><a href="http://fileti.ufabc.edu.br">http://fileti.ufabc.edu.br</a><br>
<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 26 Aug 2010 09:32:06 -0300<br>
From: Eudes Fileti <<a href="mailto:fileti@ufabc.edu.br">fileti@ufabc.edu.br</a>><br>
Subject: [gmx-users] Dipeptide generation problem<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<AANLkTikWxuC1g8fQ=fqnPfiXSWaDSTsPha=<a href="mailto:9QjPTDY38@mail.gmail.com">9QjPTDY38@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Hello everybody,<br>
I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue.<br>
This dipeptide has a positively charged site (NH3+) and a negatively charged<br>
site (COO-).<br>
My PDB file ( <a href="https://sites.google.com/site/fileti/" target="_blank">https://sites.google.com/site/fileti/</a> ) does not seem to be<br>
consistent<br>
and produces error when I execute pdb2gmx.<br>
<br>
The link above presents the PDB and the error message from pdb2gmx<br>
(which I have not found similar in the forum).<br>
<br>
Could someone give me a hand with that?<br>
<br>
Bests<br>
eef<br>
_______________________________________<br>
Eudes Eterno Fileti<br>
Centro de Ciências Naturais e Humanas<br>
Universidade Federal do ABC — CCNH<br>
Av. dos Estados, 5001<br>
Santo André - SP - Brasil<br>
CEP 09210-971<br>
+55.11.4996-0196<br>
<a href="http://fileti.ufabc.edu.br" target="_blank">http://fileti.ufabc.edu.br</a><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100826/0cfce19f/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100826/0cfce19f/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 26 Aug 2010 08:36:24 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Dipeptide generation problem<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4C765FC8.4020306@vt.edu">4C765FC8.4020306@vt.edu</a>><br>
Content-Type: text/plain; charset=windows-1252; format=flowed<br>
<br>
<br>
<br>
Eudes Fileti wrote:<br>
> Hello everybody,<br>
> I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue.<br>
> This dipeptide has a positively charged site (NH3+) and a negatively<br>
> charged site (COO-).<br>
> My PDB file ( <a href="https://sites.google.com/site/fileti/" target="_blank">https://sites.google.com/site/fileti/</a> ) does not seem to<br>
> be consistent<br>
> and produces error when I execute pdb2gmx.<br>
><br>
> The link above presents the PDB and the error message from pdb2gmx<br>
> (which I have not found similar in the forum).<br>
><br>
> Could someone give me a hand with that?<br>
><br>
<br>
Your .pdb file contains various broken residues (ASP, LYS) and non-sequential<br>
numbering (i.e., those broken residues are all numbered 1). Clean up the .pdb<br>
and try again.<br>
<br>
-Justin<br>
<br>
> Bests<br>
> eef<br>
> _______________________________________<br>
> Eudes Eterno Fileti<br>
> Centro de Ciências Naturais e Humanas<br>
> Universidade Federal do ABC — CCNH<br>
> Av. dos Estados, 5001<br>
> Santo André - SP - Brasil<br>
> CEP 09210-971<br>
> +55.11.4996-0196<br>
> <a href="http://fileti.ufabc.edu.br" target="_blank">http://fileti.ufabc.edu.br</a><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><br></blockquote></div>