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
Hi Francesco, Chimera tries to figure out atom types, but in this case they need to be adjusted before you further process the molecule (addh, addcharge, ...). Open your file pyrazine.pdb and label with Chimera atom types, for example with the commands: labelopt info idatmType label Then you can see the carbons are C2 and the nitrogens Npl. Instead you want Car and N2. The atom types are described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html> I would use the comand "setattr" to change the atom types, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> for example: sel @/idatmType=C2 setattr a idatmType Car sel sel @/idatmType=Npl setattr a idatmType N2 sel label ( ** The labels don't change automatically, you have to "label" again to see the changes. **) Now the molecule should behave as expected. Actually instead of using a separate program to build the molecule or building it up step by step in Chimera, it is much easier to look up a CID in PubChem and fetch from Pub3D, for example for pyrazine: open pubchem:9261 ...or specify with a SMILES string and use the smi23d web server, for example: open smiles:n1ccncc1 However, these both currently have the same atom type problem. We will try to improve the automatic atom type assignment - sorry about that. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
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
participants (3)
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Elaine Meng -
Eric Pettersen -
Francesco Pietra