Query about adding charge to ligand
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
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@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
Thanks a lot. On Thu, Apr 8, 2021 at 9:06 PM Elaine Meng <meng@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@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
participants (2)
-
Elaine Meng -
Nirban Dey 19MSM0098