AMBER Archive (2003)

Subject: Xleap: 'triangular' and 'square' bond

From: Christian Gossens (christian.gossens_at_epfl.ch)
Date: Thu May 22 2003 - 05:58:51 CDT

Dear Amber users,

I'm trying to parameterize raughly an organometalic complex. The metall
center is coordinated to all the 6 carbon atoms of a benzene ring and to
three other ligands.
1.) Is it correct that I can't create more than 6 bonds from the metall
center towards my 9 ligand-atoms?
2.) When binding only 3 carbon atoms of the benzene ring to the metal
center and adding some new parameters that xleap asked me for, I
encountered finally the following problem:

> saveamberparm GOSS test.top test.crd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
1-4: angle 1 27 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 1 31 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 1 34 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 26 29 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 26 32 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 29 32 duplicates bond ('triangular' bond) or angle ('square' bond)
Building improper torsion parameters.
  total 2 improper torsions applied
Building H-Bond parameters.
Marking per-residue atom chain types.
   (Residues lacking connect0/connect1 -
    these don't have chain types marked:
         res total affected
         MOL 1
   )
  (no restraints)

After printing this message xleap does write .top and .crd files. The
md-runs look reasonable.
I had a look in the code-file "unitio.c" but still don't understand.
- What do the numbers mean? An angle between 2! atoms (e.g. angle 1 27)?
- What is a triangular or square bond?
- How can I find out what improper torsons were applied?

Can anybody help? Can I just ignore these messages? Thank you very much in
advance!

Christian