[Chimera-users] help please!

Nathan Goldfarb natgoldfarb1 at gmail.com
Thu Oct 5 15:24:33 PDT 2017


Thanks so much for your help. I will try your suggestions!

Best wishes,


On Thu, Oct 5, 2017 at 9:58 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Nathan,
> Sorry, point charges are calculated using Amber's Antechamber module
> (included with Chimera), which does not handle boron.
> Note that Antechamber/GAFF (GAFF refers to the atom types it assigns) are
> meant to handle most small organic molecules, but not metal complexes,
> inorganic compounds, or unstable species such as radicals, and may not work
> well on highly charged molecules.  GAFF allows parametrization of most
> organic molecules made of C, N, O, H, S, P, F, Cl, Br and I.
> <http://ambermd.org/antechamber/gaff.html>
> I tried a boronic acid and I got a different error message than what you
> reported, but halting charge calculation with either method in Antechamber.
> In the case of not being able to calculate charges with Antechamber, we
> list some other resources and approaches in the last two sections of this
> page:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/
> addcharge.html#sources>
> I note that Pubchem3D (which includes charges) mentioned in the last
> section will not include your boronic acid because it also covers only H,
> C, N, O, F, Si, P, S, Cl, Br, and I.
> You may have to resort to more labor-intensive approaches (say QM) to
> derive point charges, or “fudge” them somehow from similar organic
> molecules, depending on the level of accuracy you are shooting for.  Sorry
> I don’t have an easy solution.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Oct 4, 2017, at 3:37 PM, Nathan Goldfarb <natgoldfarb1 at gmail.com>
> wrote:
> >
> > Hello:
> > I am trying to prep my ligand which is a tripeptide ending with a
> boronic acid. Chimera will not let me assign charges to it.  It does not
> like the boron and says there is no Sybyl equivalent in the error message.
> > Do you know how to get around this problem?
> > Thanks!
> > --
> > Nathan E. Goldfarb, M.S., Ph.D.
> > Assistant Professor of Biochemistry
> > 904-716-7339

Nathan E. Goldfarb, M.S., Ph.D.
Assistant Professor of Biochemistry

[image: LinkedIn] <http://www.linkedin.com/in/nathangoldfarb>
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