Dear Narinder, Your simulation used a water model like TIP3P that includes an H-H bond. However, you can get rid of such bonds with command: ~bond H This would remove any bonds with both ends element H. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 12, 2018, at 12:12 PM, NARINDER Kaur Harika <nkaur1@student.gsu.edu> wrote:
Dear Sir/Ma'am,
I hope you are doing good. I am interested in making MD movie from AMBER trajectory in chimera 1.12 version. Unfortunately when I load prmtop and mdcrd files in MD movie, it shows default bond between hydrogens of water molecule. I dont want to show this bond while presenting my research at meetings so I would be really grateful if I can get any help regarding removing this unwanted bond in water molecules. For further clarity I have attached avi movie file of small section of my trajectory. Thank you very much for your help and support.
With Regards, Narinder Kaur Harika Georgia state university