Re: AMBER: Joining residues/units

From: David A. Case <>
Date: Thu, 24 Feb 2005 12:54:37 -0800

On Thu, Feb 24, 2005, Bogos Agianian wrote:
> 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.

> The problem is that when I load a pdb containing the protein and the two
> ligand residues (with TER in between) xleap does not recognize/make the C-N
> peptide bond.

Don't put the TER card in there: TER cards are only supposed to go between
residues that are *not* to be covalently attached. If things are OK, leaving
out the TER card should do what you want it to (as I understand what you have


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Received on Thu Feb 24 2005 - 21:53:00 PST
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