[modeller_usage] Fwd: (My) problems with BLK

["Francesco Pietra" <>]

The log file reported no error and there were no clashes, though (I
recognized later) with a variety of sets for the soft-sphere for
chloride, the chloride ligand was displaced from the protein, along
its longest axis, by about 100A.

Perhaps, this route with "real" HETATM residue is too hard for me.
Therefore, I go back to initial results from using BLK in building the
trimer. There, the main issue was the continuous naming of residues,
and wrong position of (uncessary) TER before HEATM. For subsequent
work, I need that each chain starts from 1. Minor problem of writing a
Python script.

That "BLK route" set the chloride ligand in accordance with X-ray
diffraction data for the protein.

Thanks
francesco


---------- Forwarded message ----------
From: Francesco Pietra <>
Date: Sun, Sep 7, 2008 at 10:33 AM
Subject: Fwd: (My) problems with BLK
To: modeller <>


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 <>
Date: Sat, Sep 6, 2008 at 5:09 PM
Subject: (My) problems with BLK
To: modeller <>


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