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 [image: LinkedIn] <http://www.linkedin.com/in/nathangoldfarb>
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@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
Elaine- Thanks so much for your help. I will try your suggestions! Best wishes, Nathan On Thu, Oct 5, 2017 at 9:58 AM, Elaine Meng <meng@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@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 904-716-7339 [image: LinkedIn] <http://www.linkedin.com/in/nathangoldfarb>
participants (2)
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Elaine Meng -
Nathan Goldfarb