Le 14/04/2014 07:08, FyD a écrit :
> Dear Jean-Patrick,
>
> Yes two atoms in a given residue cannot share the same name _when
> building a force field library_. You could try R.E.D. Server
> Development/R.E.D. Python at
> http://q4md-forcefieldtools.org/REDS-Development/ to give you some
> ideas; providing a PDB file with 'elements' as atom names.
>
> R.E.D. Python does automatically correct atom names if redundant atom
> names are found; See the documentation:
> http://q4md-forcefieldtools.org/REDS-Development/Documentation
> http://q4md-forcefieldtools.org/REDS-Development/Documentation/Project.config
>
> # Correct the atom names of molecule'$n' so that two atoms in a given
> residue cannot share the same name:
> # If not provided in the 'Project.config' file MOLECULE'$n'-ATMCOR =
> ON1 by default
> # If MOLECULE'$n'-ATMCOR = ON1 only redundant atom names are renamed
> # If MOLECULE'$n'-ATMCOR = ON2 all the atoms are renamed so that an
> atom name is composed by its chemical element and an integer, which is
> automatically incremented
> # If MOLECULE'$n'-ATMCOR = OFF atom names are not corrected, when
> duplicates are found (not recommended).
> MOLECULE1-ATMCOR = ON1
>
> Here to name the atoms or rename redundant names you could use your
> own empirical rules; or an atom name can be composed of the chemical
> element (1 or 2 characters in capital_?) + an integer, which is
> automatically incremented...
>
> regards, Francois
>
>
>> 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.
>
>
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Dear Francois,
You said :
"Here to name the atoms or rename redundant names you could use your own
empirical rules; or an atom name can be composed of the chemical element
(1 or 2 characters in capital_?) + an integer, which is automatically
incremented..."
I can do this pretty easily. I actually tried to replace the name of
each atom (they are basically C, O, H and N, but duplicated) by an
integer only, that didn't work.
What are the rules for an atom name ? Does it need to contain a letter ?
Thanks anyway for your detailled answer
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Received on Mon Apr 14 2014 - 00:30:02 PDT
