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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Received on Sun Apr 13 2014 - 22:30:02 PDT
