[Chimera-users] Feature to remove default bond between hydrogen atoms of water while loading MD trajectory

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 12 14:09:30 PST 2018

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 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 at 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 

More information about the Chimera-users mailing list