Francesco Pietra wrote: > I posted to a wrong list of Modeller, so I got no answer. Here the > latest from my efforts, trying with a single chain to simplify. > > My pdb file ends like: > > HETATM 3346 CLA BLK A 859 78.668 51.520 63.082 1.00 26.90 CLA > END
The name of the residue in the PDB does not matter to Modeller if you use the BLK residue type in the alignment - it'll preserve whatever is in your input PDB. So in most cases it makes more sense to leave the original PDB names (the official atom name, residue name, and element are all 'CL' according to PDB).
> Models are built as if they had good DOPE score, though the log file complains: > > iup2crm_280W> No topology library in memory or assigning a BLK residue. > Default CHARMM atom type assigned: CLA --> CT2 > This message is written only for the first such atom. > > Although I am unfamiliar with CHARMM (I use Amber), I understand that > my setting of BLK is incorrect, CLA is represented by a wrong atom > type (CT2 stands for some carbon?). I tried variants, vainly.
Exactly - since atoms in BLK residue have no topology, Modeller does not know their type, so it guesses from the atom name. CT2 is one of the CHARMM carbon atom types (see modlib/top.lib). The only solution here is to define the topology for this residue type yourself, as covered in the FAQ. But that probably doesn't buy you much, since chloride ion is just a point - all you'll get is a subtly different VDW radius. As for the actual value of that radius, that is something that you will have to determine for yourself. LJ well depth parameters are less important since by default soft sphere is used anyway (which has the radius as its only atom-specific parameter).
> What I am trying is to represent CLA (chloride ion) as accurately as > possible, even if I am aware that the effective spatial situation > depends on the environment (in particular the balance between ionic > and covalent bonding) so that any set of literature data for CLA will > hardly fit accurately my situation.
Modeller does not use electrostatics by default anyway, so your ionic bonding will hardly be accurate. (You could certainly add individual electrostatic interactions as restraints, however.)
Ben Webb, Modeller Caretaker