Hi,
On Mon, Jan 15, 2018 at 10:27 PM, Meng Wu <wumeng.shanghaitech.edu.cn> wrote:
> I want to calculate the distance between a atom and the center of geometry of a protein in MD trajectories. I have imaged the center of geometry to origin and tried ‘distance’ command in cpptraj, but I don’t know how to write mask of the center or the origin, could anybody give me some advices about this or other ways to get what I want? Thank you in advance!
Use 'distance <protein mask> <atom mask> geom' in cpptraj, where
<protein mask> is the mask of your entire protein, <atom mask> is the
mask selecting the atom of interest, and 'geom' is the keyword that
means "use the center of geometry of the atoms in the mask".
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Jan 16 2018 - 07:00:04 PST
