[gmx-users] Dipeptide generation problem

[Justin A. Lemkul]

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
> 

-- 
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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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