Thank you so much sir for your response. It was very helpful. Kind regards On Sun, 14 Jan 2024, 21:56 Elaine Meng, <meng@cgl.ucsf.edu> wrote:
This information is in the Help page for this tool.
You can click the Help button on the "Minimize Structure" dialog or see the copy on our website here: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize...
Specifically, see the section "Force Field Parameters" and "nonstandard residues" < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize...
Short answer is that is uses GAFF (see details in link above) with the type of charges you chose in the dialog, from your image Gasteiger.
I hope this helps, 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 Jan 13, 2024, at 1:33 AM, Prabuddha Bhattacharya via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Sir
I would be grateful if you kindly let me know what force field is used by Chimera to optimize the geometry of a small organic molecule (not peptide) if I minimize the structure using the parameters as shared in the attached file.
Thank you
Kind regards
Prabuddha Bhattacharya