AMBER: principal mask dorotation

From: Esther Brugger <>
Date: Thu, 5 Apr 2007 14:46:51 -0700 (PDT)

Dear Everyone,
 I try to use "principal mask dorotation" in Ptraj to align my molecule. Because the input trajectory is very large, I seperated them into 4 input files with 2500 frames in each of them, then use this command to get the output trajectory file. But after run it, I find these 4 output structures locate at different position. The 2nd, 3rd and 4th files are close, but the 1st trajectory file is a little bit far from them. I dont' know why. And also I find some frames "jump". So I am just wondering whether this alignment is correct. Is there anybody has this experience before? Any suggestions will be appreciated.
 Also I have another question. Actually, I want to calculate the "moment of intertia" of the molecule. I tried the "vector ...principal" command in the Ptraj, I found the coordinate of the structure didn't changed after run this command. What is the difference between this command and "principal"? And I don't know which column in the output file is corresponding to the Ix, or Iy, Iz. Or the eigenvalues in each frames are the Ix, Iy and Iz (if it is diagonalized).
 Thanks a lot!

Esther B.

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Received on Sun Apr 08 2007 - 06:07:30 PDT
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