Quoting Lili Peng <lilipeng.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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Received on Sun Jul 29 2007 - 06:07:47 PDT
