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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