Thank you very much for your help Elaine. With Regards, Narinder Kaur ________________________________ From: Elaine Meng Sent: Monday, February 12, 2018 4:09:30 PM To: NARINDER Kaur Harika Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Feature to remove default bond between hydrogen atoms of water while loading MD trajectory 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 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