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
In the ali file, CLA is represented as a dot "." in both the structure and the sequence, without "/", i.e., CLA is in the same chain.
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.
I looked at toppar files on the web, being unable to find the ten-entries long range and 1-4 non-bonded soft sphere terms for CLA to introduce in my /modlib/modeller/radii.lib. Such parameterization is available for SOD (just to talk about a single-atom ion) both on the toppar files and in Modeller itself, just in the radii.lib and radii14.lib.
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.
Thanks
francesco