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<p style="margin-top:0;margin-bottom:0">Thank you very much for your help Elaine.
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<p style="margin-top:0;margin-bottom:0">With Regards, <br>
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<p style="margin-top:0;margin-bottom:0">Narinder Kaur <br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Monday, February 12, 2018 4:09:30 PM<br>
<b>To:</b> NARINDER Kaur Harika<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Feature to remove default bond between hydrogen atoms of water while loading MD trajectory</font>
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<div class="PlainText">Dear Narinder,<br>
Your simulation used a water model like TIP3P that includes an H-H bond. However, you can get rid of such bonds with command:<br>
<br>
~bond H<br>
<br>
This would remove any bonds with both ends element H.<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Feb 12, 2018, at 12:12 PM, NARINDER Kaur Harika <nkaur1@student.gsu.edu> wrote:<br>
> <br>
> Dear Sir/Ma'am, <br>
> <br>
> I hope you are doing good. <br>
> I am interested in making MD movie from AMBER trajectory in chimera 1.12 version.
<br>
> 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.<br>
> For further clarity I have attached avi movie file of small section of my trajectory.
<br>
> Thank you very much for your help and support.<br>
> <br>
> With Regards, <br>
> Narinder Kaur Harika<br>
> Georgia state university <br>
<br>
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