Le 13/04/2014 22:30, Bill Ross a écrit :
> 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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I would basically like to do one of the things you suggested. There is a
way to name the atoms, one by one, in the software I use (I use
Avogadro, I'm on Archlinux).
I can not put the atom names in the smile string.
But if you knew a software which can do what I want, that would be great.
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Received on Sun Apr 13 2014 - 15:30:02 PDT
