AMBER Archive (2005)

Subject: Re: AMBER: Joining residues/units

From: FyD (fyd_at_u-picardie.fr)
Date: Fri Feb 25 2005 - 11:13:29 CST

> I am trying to use amber7 to simulate a ligand-protein system. The ligand
> contains a sugar (MurNAc) and a peptide.
>
> For some reason, I decided to split the ligand into two UNITS, one containing
> the sugar and the other one the peptide. The split point is a peptide bond,
> ie. one UNIT ends in C=O and the other in N-H. I created lib files for the
> two UNITS based on glycam04 and ff99 and when I load the UNITs in xleap
> everything seems OK.

OK

> The problem is that when I load a pdb containing the protein and the two
> ligand residues (with TER in between)

OK

> xleap does not recognize/make the C-N
> peptide bond. Note that I had set the proper tail and head atoms when the
> UNITs were created, so tail of UNIT 1 the C of C=O and head of UNIT 2 the N
> of N-H.

If you have a branched system, you need to make the bond with the "bond"
command...

> Then I tried the bond command and this seems to work, but looking at the
> prepin file outputed the impropers for the peptide plane were wrong.

I think you should provide more info. for that. I think the way you proceeded is
correct. There is a trick somewhere ;-)

"peptide plane were wrong", you mean in your unit ? Usually the conformation in
the UNIT does not matter, but only the conformation in your whole initial PDB
file is important. Then, if you have the same residue/atom names in your PDB
file and in your unit, LEaP will match both...

> I also tried to connect the two UNITs with the sequence command but when I
> load the merged UNIT xleap crashes. Note that some atoms of the two UNITs I
> created have common naming.
>
> How can I make xleap join/merge the two UNITs into one ligand UNIT with a
> proper peptide bond?

You system is quite complicated. You should provide more info to get help. You
can send me you data and I would be interested to look at your problem.

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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