I succeeded in defining chloride anion as a real residue. Modeller run without errors. However, I set arbitrary values (2.50A) for the terms "long range and 1-4 non-bonded soft-sphere terms". I was unable to find such terms for any single-atom anion. Also I was perplexed to see 1.90-1.95A for sodium ion and 0.72A for Mg++; why such a big difference?. Do you know such values for single-atom anions, in particular chloride? Or the original work dealing (and showing) how to compute such terms. I am equipped for ab initio calculations, if needed.

I understand that BLK usage (where I was unsuccessful, as reported on my previous mail) would be enough in this case. But I am curious to test, if not else to learn how to deal with real non-standdard residues.

I asked about such ten terms on the CHARMM forum. The moderator refused to answer the question for non-CHARMM use and made also comments - to this respect - that it is better to forget.

Thanks francesco

---------- Forwarded message ---------- From: Francesco Pietra chiendarret@gmail.com Date: Sat, Sep 6, 2008 at 5:09 PM Subject: (My) problems with BLK To: modeller modeller_usage@salilab.org

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

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