Hi,
Slight modification; do 'vector center <mask>' - that will give you
the center of mass of the atoms selected by <mask>.
-Dan
On Tue, Apr 9, 2024 at 10:56 AM Dickson, Callum via AMBER
<amber.ambermd.org> wrote:
>
> Hi Fulbabu,
>
> You can use the "vector" command in cpptraj.
>
> For example, here would be the command for residue 1:
>
> vector c0 :1 :1 out c0.out
>
> This will give you the x,y,z coords for residue 1 per frame into c0.out.
>
> Best,
> Callum
>
>
> -----Original Message-----
> From: Md Fulbabu Sk via AMBER <amber.ambermd.org>
> Sent: Monday, April 8, 2024 6:35 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Printing X Y Z coordinates of selected atom or group of atoms in cpptraj
>
> !-------------------------------------------------------------------|
> This Message Is From an External Sender
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> |-------------------------------------------------------------------!
>
> Hi AMBER Community,
>
> I would like to calculate the Z-position of a selected residue throughout the trajectory. Is there a way, such as using a cpptraj command, to calculate this and print it to a text file for each frame of the MD trajectory? I'm interested in obtaining the X, Y, Z coordinates of a selected atom (or the average coordinates of a selected group of atoms).
>
>
> Thanks
>
> Fulbabu
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Received on Tue Apr 09 2024 - 09:30:02 PDT
