Re: [AMBER] visualizing first mode of motion from PCA analysis in chimera or vmd

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Fri, 9 Jun 2017 04:46:55 +0000

Hi,

VMD in windows does not work with netcdf format trajectories.


                   Best Regards

[photo]



Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy


A Kalina, Santacruz [E], Mumbai 400098, INDIA
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________________________________
From: Thakur, Abhishek <axt651.miami.edu>
Sent: 09 June 2017 02:46:38
To: amber.ambermd.org
Subject: [AMBER] visualizing first mode of motion from PCA analysis in chimera or vmd

Hi

Using the tutorial on amber website

http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/pca-cpu-gpu.cpptraj


I have generated the cpu-gpu-modes.prmtop and cpu-gpu-modes.nc to analyze the

first mode of motion in chimera or VMD.

But I am unable to see anything on these softwares. Can anyone guide me how to visualtize it?



Thaning you,
Abhishek

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Received on Thu Jun 08 2017 - 22:00:03 PDT