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 - 13:00:03 PDT
