AMBER Archive (2004)

Subject: Re: AMBER: Ptraj data

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Tue Sep 21 2004 - 13:59:58 CDT

> 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).

If I understand you correctly, you want the data to be "ps" vs. time
rather than "frame #" vs. time. This can be accomplished via the time
keyword to RMS as you've used. It is possible that this is not being
parsed correctly? Also, I think you want the time to be 50.0 not 0.5; try
moving the time keyword and value before the mask...

> rms first out N25D3_data1 :1 time 0.5

rms first out N25D3_data1 time 50.0 :1

(Also, I am not clear exactly how much information you will obtain from
doing the best fit RMSd of a single residue; I guess this might give
insight into flips to different conformations?)

Good luck and let us know if you have further questions.

--tom

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