Feature to remove default bond between hydrogen atoms of water while loading MD trajectory
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
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
Thank you very much for your help Elaine. With Regards, Narinder Kaur ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> 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 <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
participants (2)
-
Elaine Meng -
NARINDER Kaur Harika