Dear Bhanu, It is whatever atoms are in the structure. There is no implicit solvent. So whatever waters are in the structure, or that you have added to the structure (see Tools... Structure Editing... Solvate) would be included. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/solvate/solvate.ht...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize....> For the future, questions about using Chimera should be sent to chimera-users@cgl.ucsf.edu. This chimera-dev@cgl.ucsf.edu list is for questions about writing code (python etc.). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 3, 2020, at 9:14 AM, Bhanu Sharma <bhanukumar331@gmail.com> wrote:
Dear sir/mam I am using the AMBER module in Chimera. I just want to know that when we minimize energy of a protein structure using AMBER in chimera then is it done in vacuum or in solvent. I also googled it but did not find a satisfactory answer. Please help me. _ _
Best regards,
Bhanu sharma