AMBER Archive (2007)

Subject: Re: AMBER: adding organic molecule to polypeptide residue

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Jul 28 2007 - 04:05:18 CDT

Quoting Lili Peng <lilipeng_at_gmail.com>:

> I'd like to know how I can attach an organic molecule to a residue on a
> polypeptide chain. I have two PDB files, one for the organic molecule and
> the other for the chain. I tried to link the two molecules together in
> Accelrys' DS Visualizer program, but it won't let me create chemical
> reactions. Is there a way I can do this in AMBER, like using tleap? I read
> in the AMBER archive about specifiying .lib files, but I'm not sure if this
> is the direction I should pursue.

It depends by what you mean by attach an "organic molecule to a residue on a
polypeptide chain". Let's take an example of an aromatic ring bound to
Gln or Asn by a peptide bond. You can split your system into two
fragments, i.e. two force field libraries: Asn + Aro in such way:

Asn_sidechain-CONH-Aromatic

To do so, you can start from these two whole molecules:

Asn-CO-NHMe + MeCO-NH-Aro
        <--> <-->
  intra-molecular charge constraint set to zero

In RED-III this is really straightforward. You set up your system
using the INTRA-MCC keyword for each molecule and you use 2 P2N files:
Mol_red1.p2n and Mol_red2.p2n for the 2 molecules. You get all in a
single RED-III run, the library is a Tripos mol2 file format.

You can also imagine other similar strategies for other type of linkage...

regards, Francois

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