[Chimera-users] Query about adding charge to ligand

Nirban Dey 19MSM0098 nirban.dey2019 at vitstudent.ac.in
Thu Apr 8 21:47:26 PDT 2021

Thanks a lot.

On Thu, Apr 8, 2021 at 9:06 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Nirban,
> The Gasteiger and AM1-BCC charge calculations are completely different and
> so it is not a surprise that one method "works" on a molecule and the other
> does not.  The Gasteiger method is more simplistic and faster.  The AM1-BCC
> method is more intensive but will more often fail, especially on larger or
> more highly charged molecules.  We (the Chimera developers) did not create
> these methods.
> If you really want to know how they work, read the original publications...
>         • AM1-BCC - semi-empirical (AM1) with bond charge correction (BCC)
> Fast, efficient generation of high-quality atomic charges. AM1-BCC model:
> II. Parameterization and validation.
> Jakalian A, Jack DB, Bayly CI. J Comput Chem. 2002 Dec;23(16):1623-41. <
> https://pubmed.ncbi.nlm.nih.gov/12395429/>
>         • Gasteiger - faster method based on atom types and connectivity
> Iterative partial equalization of orbital electronegativity—a rapid access
> to atomic charges. Johann Gasteiger, Mario Marsili. Tetrahedron. Volume 36,
> Issue 22, 1980, Pages 3219-3228
> <https://www.sciencedirect.com/science/article/pii/0040402080801682>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Apr 8, 2021, at 4:38 AM, Nirban Dey 19MSM0098 <
> nirban.dey2019 at vitstudent.ac.in> wrote:
> >
> > Hello, I am a Masters student of VIT University India. I am using
> chimera to prepare my ligand. In the add charge option I noticed that if my
> ligand has negative or positive charge and I try to add AM1-BCC it gives
> error but I can add Gasteiger charge. Even if I set charge to +0 for the
> ligands that have charge like -1 or +1  and try to add  AM1-BCC it gives
> error. I want to know what is the reason that Gasteiger charge can be added
> but AM1-BCC cannot be added..Kindly help me in this regard.
> > Thanking You
> > Nirban
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