[Chimera-users] Pyrazine problem

Francesco Pietra chiendarret at gmail.com
Mon Sep 15 07:39:28 PDT 2008

I am dealing with pyrazine compunds in view of docking with DOCK6. The
two nitrogens proved problematic for Chimera so  that, to simplify, I
tried with pyrazine itself, getting the same problems.

I used for getting the pdb the MM package I am familiar with:
1.  draw benzene,
2. replace two para carbons with N,
3. replace the H on N with a lone pair.

The two nitrogens are now indicated of MM3 (or MMX) type 37 (-N=C-/PYR
(DELOCALIZED). The charge on the nitrogens is 0.15, on the lone pairs
-0.21, on carbon 0.14, on H 0.04.

Save as pdb, load to Chimera, then Tools, Structure editing .. Add
charge, it results total charge -2. In fact, commanding addH adds a
hydrogen to each nitrogen and the resulting molecule is neutral, while
it should be +2.

If in Chimera I save the loaded pdb as mol2, the two nitrogens result
of Tripos type N.pl3, i.e., trigonal planar nitrogen, which is the
wrong type. Naively, I replaced N.pl3 with N.ar (aromatic nitrogen) in
the mol2.file, getting the same results on reloading the mol2.

So the two packages, MM and Chimera are internally consistent but (for
the first time in my experience with both packages) they are not
mutually consistent.

I tried to build pyrazine atom-by-atom, getting the same results.

Attached is the pdb and the mol2. When opening the pdb, Chimera says:
"Ignored bad pdb record found on line 26"; actually there are fewer
than 26 lines.

Thanks for help

francesco pietra
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