Dear Rezvan,
> I want to have the parameters for antibiotics bonded to ribosomes. I
> was wondering if I have to use ANTECHAMBER?
You can use Antechamber and/or R.E.D. (or R.E.D. Server) at
http://q4md-forcefieldtools.org.
I would like to suggest you to use R.E.D. (or R.E.D. Server). If your
antibiotics are connected through a bond to a larger system, I suggest
you twice to use R.E.D. ;-) as you will have to define charge
constraints during the charge fitting step.
> I mean shall I produce the parameters myself?
If they are not available: Yes
> Have it been done before? Do parameters for antibiotics already
> exist in a par/topology file?
In general you start from a PDB file and you generate a FF library
(off, mol2 or prep format) using R.E.D. or Antechamber for your
molecule; you load this new FF library in the LEaP program (with the
FF you wish to use) and create the prmtop/prmcrd files for your entire
molecular system for MD simulation.
Concerning using R.E.D. see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
or
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
> By the way, I am not still sure. To use the ANTECHAMBER do I need to
> buy the AMBER program?!
Antechamber and R.E.D. are provided at no cost; R.E.D. is free.
Antechamber is in the AmberTools (most of these tools are free).
regards, Francois
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Received on Wed Sep 05 2012 - 00:30:03 PDT
