[Chimera-users] trying to add charges

Irene Newhouse einew at hotmail.com
Wed Apr 27 17:16:28 PDT 2011

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"...


> Subject: Re: [Chimera-users] trying to add charges
> From: meng at cgl.ucsf.edu
> Date: Wed, 27 Apr 2011 17:11:36 -0700
> CC: einew at hotmail.com
> To: chimera-users at 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
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