The Chimera interface is meant to be simple and handle most small organic molecules automatically. However, when the automatic parametrization does not handle whatever compound or element you need to model, then you will have to use some other program or method. You may need to look carefully at the documentation for whatever docking program you are using, and then manually edit whatever data files that docking program uses to put in the parameters that you want. You would also need to figure out what values are appropriate, which might be available in published papers. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 11, 2024, at 7:56 AM, turgut şekerler via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Chimera Team,

I hope this message finds you well. I am writing to inquire about an issue I encountered while attempting to perform docking with a selenium atom using the Dock Prep module in Chimera.

My goal is docking selenium atom and my target protein. But ı always get a error message : cant prepare ligand.

I have been utilizing Chimera's Dock Prep module to prepare ligands for docking with proteins, and it has been an effective tool thus far. However, I have encountered difficulties when attempting to prepare a ligand containing a selenium atom. It seems that the Dock Prep module is unable to handle the selenium atom properly, resulting in errors during ligand preparation.

I have attempted to troubleshoot this issue by researching error codes and exploring potential solutions, but I have been unable to find a resolution. As such, I am reaching out to inquire if there are any specific recommendations or alternative approaches that could be used to successfully prepare a ligand containing a selenium atom for docking in Chimera.

I understand that Chimera utilizes standard force field parameters for ligand preparation, but given the unique properties of selenium, it may be necessary to consider additional or specialized parameters to ensure accurate docking results.

Any guidance or assistance you could provide on this matter would be greatly appreciated. I am eager to resolve this issue and continue utilizing Chimera for my docking studies.

Thank you for your attention to this matter. I look forward to your response.

Sincerely,