Look for Lysine in amino12.lib instead. The OFF file format is documented
here: http://ambermd.org/doc/OFF_file_format.txt
On Mon, Apr 14, 2014 at 2:57 PM, Jean-Patrick Francoia <
jeanpatrick.francoia.gmail.com> wrote:
> 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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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Apr 14 2014 - 12:30:04 PDT
