[Chimera-users] trying to add charges

[Elaine Meng]

Hi Irene,
One more idea. You could search the Zinc database:
<http://zinc.docking.org/>
which has tons of compounds in Mol2 format with charges.  I looked up FPS, but by a rather circuitous process (and maybe there is a shorter one):

(1) looked up FPS in PDB's Ligand Expo to verify it is farnesyl thiopyrophosphate
<http://ligand-expo.rcsb.org/ld-search.html>
(2) looked up that compound in PubChem to get a SMILES string:
CC(=CCCC(=CCCC(=CCSP(=O)([O-])OP(=O)([O-])[O-])C)C)C
(3) entered SMILES string in Zinc search field

I couldn't use the SMILES from ligand expo because it was the neutral form rather than -3 charged.  You could use a similar process for IPE, at least if it's in the Zinc database.  For Mg++ you would just edit in +2 as the charge in the Mol2 file.

I attached the Mol2 file, but you should doublecheck to make sure it is actually the right molecule.  Also, I don't recall the process by which Zinc determines charges, so you may want to look into that to see if it is adequate for your purposes.

Also, there is still a problem.  You have to figure out which atoms in this mol2 correspond to which ones in your structure, which is undoubtedly in a different position and conformation. So I don't know if this whole process is worth it!

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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