Dear Jean-Patrick,
If you do want to parameterize a polymer I would like to suggest you
to use R.E.D. Server Development/R.E.D. Python at
http://q4md-forcefieldtools.org/REDS-Development/
You need to split your polymer into elementary building blocks...
See examples in R.E.DD.B.:
see
http://q4md-forcefieldtools.org/REDDB/projects/F-93/
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
http://q4md-forcefieldtools.org/REDDB/projects/F-60/
Tutorials at
http://q4md-forcefieldtools.org/Tutorial/
Finally the OFF library file format has advantages, but also limitations;
See
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
We are about to release a new version of REDS-Development/R.E.D.
Python and a new tutorial.
If you are interested I can give you the address of the new web site
and tutorial...
regards, Francois
> 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/
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Received on Mon Apr 14 2014 - 23:00:02 PDT
