AMBER Archive (2005)

Subject: AMBER: Joining residues/units

From: Bogos Agianian (agianian_at_embl.de)
Date: Thu Feb 24 2005 - 08:58:55 CST

Hi,
 
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. 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.
 
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 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?
 
 
Thanks in advance for any help
 
Bogos
 
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