Maybe the program you are using to generate pdf has an option for atom names? Unless you can put atom names in the smiles string you generate? Or try other programs to convert smiles to pdb.
Bill
-------- Original message --------
From: Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com>
Date:04/13/2014 12:40 PM (GMT-08:00)
To: amber.ambermd.org
Subject: [AMBER] Generate a pdb with unique atom names
Hello,
I am a master student, and one of my course is molecular dynamic. So, in
class we use (the old) Amber 9 to minimize some structures, for example.
Also, one of our exercices is to build the structure of a lysine polymer
with Python (a programmation language), and then to minimize the
structure with Amber.
The important thing is my Python program generates a SMILE string. I can
import this string with plenty of softwares, and then save it into the
pdb format. But in this pdb, each atom does not have a unique name, a
very common issue when using Amber.
So, I would like to know if there is a solution to assign each atom a
unique name. I have seen a lot of threads dealing about this problem on
the mailing list, but I have never seen any solution. I can't obviously
rename each atom by hand.
Sincerely
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Received on Sun Apr 13 2014 - 14:00:02 PDT
