<div dir="ltr">Thanks a lot.</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Apr 8, 2021 at 9:06 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello Nirban,<br>
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.<br>
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If you really want to know how they work, read the original publications...<br>
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• AM1-BCC - semi-empirical (AM1) with bond charge correction (BCC)<br>
<br>
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.<br>
Jakalian A, Jack DB, Bayly CI. J Comput Chem. 2002 Dec;23(16):1623-41. <<a href="https://pubmed.ncbi.nlm.nih.gov/12395429/" rel="noreferrer" target="_blank">https://pubmed.ncbi.nlm.nih.gov/12395429/</a>><br>
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• Gasteiger - faster method based on atom types and connectivity<br>
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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<br>
<<a href="https://www.sciencedirect.com/science/article/pii/0040402080801682" rel="noreferrer" target="_blank">https://www.sciencedirect.com/science/article/pii/0040402080801682</a>><br>
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I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Apr 8, 2021, at 4:38 AM, Nirban Dey 19MSM0098 <<a href="mailto:nirban.dey2019@vitstudent.ac.in" target="_blank">nirban.dey2019@vitstudent.ac.in</a>> wrote:<br>
> <br>
> 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.<br>
> Thanking You<br>
> Nirban<br>
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