Re: [AMBER] using antechamber to parapetrize non standard amino acid

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Wed, 26 Sep 2012 15:49:28 +0200

Dear Houcemeddine Othman,

I guess you want to generate a molecular fragment for your non standard amino.

You might be interested in using the R.E.D. tools or R.E.D. Server at
q4md-forcefieldtools.org.

You will find tutorials there; See for instance:
  http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
    vs
  http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
    vs
  http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
  http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
  http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17

I would use Amber99SB (or the latest update available) and not GAFF,
as Amber99SB is designed for proteins.

regards, Francois


> i aim to parametrize a non standard amino (pyroglutamic acid) acid
> before running the MD simulation.
> I intend to use openbabel for computing the partial charges of my
> residue then antechamber and parmchk to generate frcmod file. I am
> not sure if antechamber is a reliable tool to parametrize non
> standard amino acids.
> also, is GRAFF compatible with the FF96 force field?



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Received on Wed Sep 26 2012 - 07:00:06 PDT