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 ?
And what about generating my own library for my molecule ? Like they do
here:
http://ambermd.org/tutorials/basic/tutorial4b/
J-P
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Received on Mon Apr 14 2014 - 06:00:04 PDT
