[Chimera-users] Pyrazine problem

Eric Pettersen pett at cgl.ucsf.edu
Mon Sep 15 15:41:42 PDT 2008

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 Pettersen
                         UCSF Computer Graphics Lab

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>_______________________________________________
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