AMBER Archive (2005)

Subject: Re: AMBER: Joining residues/units

From: Bogos Agianian (agianian_at_embl.de)
Date: Thu Feb 24 2005 - 15:22:07 CST

Thank you very much for your answer.
 
When I remove the TER between the two ligand residues xleap crashes giving the
message:
 
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 116
!FATAL: Message: No C2 in aaOrig list
!
!ABORTING.
 
What could be wrong?
 
Thanks
Bogos
 
 
Quoting "David A. Case" <case_at_scripps.edu>:
 
> 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
> written.)
>
> ...dac
>
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