Le 14/04/2014 15:01, Jason Swails a écrit :
> On Mon, 2014-04-14 at 14:50 +0200, Jean-Patrick Francoia wrote:
>> Le 14/04/2014 14:10, Jason Swails a écrit :
>>> On Sun, 2014-04-13 at 21:40 +0200, Jean-Patrick Francoia wrote:
>>>> 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.
>>> LEaP must know about every residue defined in an input structure so it
>>> knows what atom types to apply to each atom as well as what charges to
>>> apply. To that end, the atom names of every atom must match the names
>>> in the library files so that LEaP can map the atom names to the atom
>>> types, charges, and connectivities.
>>>
>>> The atom names of the amino acid and nucleic acid residues match the
>>> atom names used by the PDB so that almost any PDB you download from the
>>> official Protein Database will work. If you are creating your own PDB
>>> from SMILES strings, you will need to fix the atom names yourself. If
>>> you are already using Python to do some file manipulations, you can use
>>> Python to write a script to rename your atoms.
>>>
>>> Alternatively, you can use LEaP to create your Lysine polymer with the
>>> "sequence" command. If you want a 3-mer of lysine residues, the command
>>>
>>> lys3 = sequence {NLYS LYS CLYS}
>>>
>>> will generate a tripeptide with 3 lysine residues.
>>>
>>> HTH,
>>> Jason
>>>
>> I can't use leap to generate the polymer, sadly. Mine is a complex one,
>> branched on the epsilon and alpha amines, with several hundreds of amino
>> acids.
>>
>> Ok I get it. But how can I know how the atoms are named in the library ?
>> What is the naming algorythm ?
> The naming scheme is the one defined by the PDB. You can see what the
> names are in the OFF library files inside $AMBERHOME/dat/leap/lib.
>
>> And what about generating my own library for my molecule ? Like they do
>> here:
>> http://ambermd.org/tutorials/basic/tutorial4b/
> This is done for individual residues (so only a single amino acid or a
> small organic molecule). You will need to break your system down into
> smaller parts to parametrize each one. But if you're using amino acids,
> why redo all the work that's already been done? Especially since you
> need to use the same charge sets that were used to generate the torsion
> parameters in the first place.
>
> HTH,
> Jason
>
Ok, I fund the file describing the lysine residue in the folder you
indicated:
pro-dna91.nmr.off
The thing is it's not commented at all.
Nobody has ever done that before ?
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Received on Mon Apr 14 2014 - 12:00:02 PDT
