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

[NARINDER Kaur Harika]

Thank you very much for your help Elaine.


With Regards,

Narinder Kaur

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, February 12, 2018 4:09:30 PM
To: NARINDER Kaur Harika
Cc: chimera-users at 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 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

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