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"... Irene
Subject: Re: [Chimera-users] trying to add charges From: meng@cgl.ucsf.edu Date: Wed, 27 Apr 2011 17:11:36 -0700 CC: einew@hotmail.com To: chimera-users@cgl.ucsf.edu
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 ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco