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Thanks again! As one of my former bosses used to say, "Anything worth doing is more trouble than it's worth" & another one used to say, "If it were EASY, it'd have been done already"...<br><br>Irene<br><br>> Subject: Re: [Chimera-users] trying to add charges<br>> From: meng@cgl.ucsf.edu<br>> Date: Wed, 27 Apr 2011 17:11:36 -0700<br>> CC: einew@hotmail.com<br>> To: chimera-users@cgl.ucsf.edu<br>> <br>> Hi Irene,<br>> One more idea. You could search the Zinc database:<br>> <http://zinc.docking.org/><br>> 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):<br>> <br>> (1) looked up FPS in PDB's Ligand Expo to verify it is farnesyl thiopyrophosphate<br>> <http://ligand-expo.rcsb.org/ld-search.html><br>> (2) looked up that compound in PubChem to get a SMILES string:<br>> CC(=CCCC(=CCCC(=CCSP(=O)([O-])OP(=O)([O-])[O-])C)C)C<br>> (3) entered SMILES string in Zinc search field<br>> <br>> 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.<br>> <br>> 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.<br>> <br>> 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!<br>> <br>> I hope this helps,<br>> Elaine<br>> -----<br>> Elaine C. Meng, Ph.D. <br>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>> Department of Pharmaceutical Chemistry<br>> University of California, San Francisco<br>> <br> </body>
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