Quoting Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com>:
> 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 ?
See
http://q4md-forcefieldtools.org/REDS-Development/Documentation/readme.txt
&
http://www.wwpdb.org/documentation/format33/sect9.html
An atom name can be constituted of 4 characters maximum;
columns 13 - 16
I would start an atom name by the chemical element.
regards, Francois
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Received on Mon Apr 14 2014 - 12:30:03 PDT
