Hi. This is directed to :
>Karsten Suhre <> (IGS)
>Introduction of a Ca binding site
>Moshe Amitay <> ("Bar-Ilan University, Ramat-Gan,
>building a model with water molecules.
From: Tjaart de Beer <>
>Modelling with metals and hetero.
The practical advice :
Modeller treats the 'hetatm' entries as residues for much of the modelling
process. By this, I mean that it is as picky as with the other residue
entries when you describe them in the alignment. You can see all the types of
residue entry that it knows about in the mod6v2/lib/restyp.lib file.
Its always simpler to 'SET HETATM_IO', rather than change the pdb file. If
modeller knows about the heteroatom residue code then it will read it, and
not attempt to attach proximal metal ions to the polypeptide backbone.
I was mislead by the chain break character '/', which actually introduces a
chain break for your model, rather than describing a corresponding template
(? not really sure here). I got away with this example :
1tem:Template:1: :3: :.:.:.
WLMzz*
1hom:Homolog:1: :3: :.:.:.
WITzz*
Where I just used set HETATOM_IO on. The important thing is the numbering used
in the PIR header for each protein sequence - this only relates to the amino
acids, not the hereroatoms.
I imagine that you need to use set WATER_IO on, and put in the waters, too,
but the chain break didn't seem to help.
Above all, look carefully at the numbers that Modeller gives you when it
complains that you don't have enough residues in the PDB file or the
sequence. For Moshe's case, the chain break may well have been the problem,
but it can't hurt to use the unedited PDB file but setting HETATM_IO as well
as WATER_IO (but maybe you could delete the un-necessary waters and
heteroatoms from the pdb file just to make the alignment simpler!).
As for the optimization behaviour with metal atoms - I didn't really notice
modeller doing any optimization of the bonding geometry, but in my case these
contacts were thoroughly conserved. However, I can't see any parameters in
the MD forcefield definitions to indicate that charge/ligand geometry is
taken into account, it is probably all done through restraints.
Think thats it - sorry for not giving a concrete example!
j--
ps. For Calcium - the HETATM's residue entry should be CAL or CA (that is, not
CA2), and '3' is the alignment symbol used in the PIR file (see the
restyp.lib file).
_______________________________________________________________________
Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics
Hamburg http://www.zbh.uni-hamburg.de/mitarbeiter/procter