AMBER: Ptraj data

From: Steve Seibold <>
Date: Tue, 21 Sep 2004 14:13:49 -0400

I have been using ptraj to get RMSd. However, when I get the data it
places the number of frames (and not the time in picoseconds) on the
x-axis. That is, I have 1000 frames with each at 2500 steps (50 ps).
When I calculate the RMSd of a residue it gives me RMSd vs 1 through
1000 frames instead of time. The tutorial, using DNA, on the AMBER web
page shows in their example that using ptraj gives the time in ps. I
would like the RMSd for every ps or so and not for each frame where each
frame consists of 50ps. Could someone help me?
I am using AMBER7 and my input file is as follows:
trajin HIV_N25D3.mdcrd

trajout HIV_N25D3_1.mdcrd nobox


box x 51.1333056 y 50.7934380 z 72.183431

center :1-99 origin

image :100-198 origin center familiar

rms first out N25D3_data1 :1 time 0.5

rms first out N25D3_data2 :2 time 0.5

rms first out N25D3_data3 :3 time 0.5

average N25D3_avg.pdb :1-99 pdb

strip :WAT



Any ideas would be greatly appreciated.

Thank you,


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Received on Tue Sep 21 2004 - 19:53:00 PDT
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