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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Apr 14 2014 - 05:30:03 PDT
