Use VMD.
-load prmtop and trajectory
-Open Graphics menu ->Labels, select Bonds in drop down menu
-Open MOUSE menu ->Label -> choose Bonds
-Click on first atom, then second atom, whose distance you want to measure
(they do NOT need to be chemically bonded)
-In the Labels panel, click to highlight the line that contains the two
atoms whose distance you want to measure.
-In the Labels panel, at the bottom select the Graph menu and select the
Show Preview option... A small graph should appear.
-Click Save... Or Graph... to export the data.
You can select Show, Hide, Delete to determine what is displayed in the
trajectory window.
Playing the trajectory can show you how the distance changes/time.
The same can be done for angles, dihedrals, etc, and the atoms do not need
to be chemically bonded.
Hope this helps,
Dean
On 8/11/11 2:53 AM, "clwg" <clwg.163.com> wrote:
>Dear Amber users,
>
> I want to calculate the distance between the N1 atom of GUA 61
>and the
>N3 atom of CYT 72 in the chain GCGATCGA(not the centre of mass). this is
>the input file *ptraj.in*
>trajin prod.mdcrd
>distance G3-C6 :61.N1 :72.N3 out G3-C6.list
>and I used excell to get the curve of distance vs
>time. To my surpriae, in the curve all the distance is
>between 2 .6A and 4A in 300kand 400k. But in fact, the distance will
>beyond 5A
>could you help me how to do that .
> Many thanks in advance.
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Received on Thu Aug 11 2011 - 12:30:03 PDT
