Right. I was computing the π electrons contributed to the ring by the nitrogens incorrectly. The fix will be in tonight's daily build. BTW, your file does have 26 lines -- the last line contains a single space character. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Sep 15, 2008, at 7:39 AM, Francesco Pietra wrote:
Hi: 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 < pyrazine .pdb><pyrazine.mol2>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users