Date: Thu, 25 Sep 2003 18:35:54 -0400 (EDT)
Subject: molecule definition
From: "GUILLERMINA L ESTIU"

Ok,
Now it is clear (for me) what has happened:
I have 3 monomers with 3 chains each

Monomer 1
Chain A
Chain B
Chain C -> bonded to Ni2OH (4 atoms)->bonded to urea (8 atoms)

The same pattern holds for the other monomers (2 and 3)

The structure of my first pdb was

Monomer1
Monomer2
Monomer3
Ni1
Ni2
Ni3
urea1
urea2
urea3

The last residue of each monomer (kcx) is explicitely bonded (trough bond
command) ot the dinickel unit, and the latter to urea 1

So, leap reads the first molecule (first chain), second (second chain) and third
(chain C). In the last one it follows the connectivities explicitely defined
and assigns 12 extra atoms to the molecule (4 of the Ni unit and 8 of urea). As
it will not move the atoms in the pdb, it assigns 12 atoms of the next residue
to the molecule. And this is how the molecule ends in the middle of a residue.

The same happens in the second molecule... and the shift increases to 24 atoms.

I wouldn't say that this is "a bug", but I believe that is something that not
everybody is aware of

The molecules are built on the basis of the connectivities (either head-tail or
explicitely defined). Leap reads, or even adds ter cards, but the explicit
definition of the connectivities (bond commands) is stronger that the ter card

In my "second version", the structure of the pdb is:

Monomer1 (chain A, chain B, chain C)
Ni1
urea1
Monomer2 (chain A, chain B, chain C)
Ni2
urea2
Monomer3 (chain A, chain B, chain C)
Ni3
Urea3

And leap built 9 molecules, one for each chain, with the Ni and urea units
included in the molecule of chainC

But leap always define 1 molecule for non-solvated systems. At least those that
I have tested

It is now clear, at least for me
Thanks for your help
Guille
Dr Guillermina Estiu