[AMBER] question about commutation of sub-trajectories and frame aligning

From: Gordon Richard Chalmers <gordoncs.uga.edu>
Date: Wed, 10 May 2017 12:56:42 +0000

Dear Amber users,

I have an odd question about frame aligning a 1000ns trajectory

of this protein st6Gal1, which has 302 residues and 4938 atoms (it is
actually st6Gal1 without the first 10 residues, to be specific for those
who know st6Gal1). I am knew to this forum; I hope I am being clear

-- The question I have is about the lack of commutation of frame

aligning and sub-trajectories. I don't know what is causing the

problem, and I am posting this to see if anybody else knows the answer

to this oddness. Thank you.

For reasons that I won't explain I am interested in the 0-200ns, 400-600ns,

and 800-1000ns segments of this 1000ns trajectory. I would like a non-pathological

aligned 0-200ns segment of the 1000ns trajectory of 500,000 frames and 4932

atoms. I have no problem with the 400-600ns and 800-1000ns segments.

There are 2 ways to get this sub-trajectory aligned. I am using the default

reference frame 1 of the 1000ns trajectory.

1) If you take a 0-200ns segment of the unaligned 1000ns trajectory and frame align

the 200ns,

- new unaligned 0-200ns trajectory

parm rST6Gal1.hLoop.reduce.nowat.nobox.prmtop
trajin rST6Gal1.hLoop.reduce.nowat.nobox.mdcrd 1 100000
trajout rST6Gal1.hLoop.reduce.nowat.nobox_0-200ns.mdcrd

- and then frame align it

parm rST6Gal1.hLoop.reduce.nowat.nobox.prmtop
trajin rST6Gal1.hLoop.reduce.nowat.nobox_0-200ns.mdcrd
rmsd first :6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,29,30,31,32,33,34,35,38,39,40,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,251,252,253,254,255,256,257,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296.CA
trajout trajectory_no_tumbling_align_0_200.crd

, then after that, the output trajectory is pathological.

e.g., Warning: Frame 54683 coords 1 & 2 overlap at origin; may be corrupt.
          Warning: Frame 54684 coords 1 & 2 overlap at origin; may be corrupt.

Apparently this procedure gives a pathological frame aligned trajectory, starting
at frame 54683.

I don't think it matters what frame it is happening it, except I know it has no
overlapping coordinates in the unaligned 0-200ns segment of the 1000ns

The unaligned 0-200ns is not corrupt and I can prove that there are no overlapping

coordinates in any frame.

-- There are only 6 degrees of freedom in frame aligning - overall translations and overall

rotations. If frame 1 does not have a problem with overlapping coordinates, then no other

frame should have this problem. There are no overlapping coordinates at frame 1.

2) However, if you frame align the entire 1000ns FIRST, and then take the 0-200ns segment

from the aligned 1000ns trajectory, then there is no problem with the aligned 0-200ns


-- Apparently, the operations of frame aligning and creating a segment does not commute

with taking a segment and then frame aligning.

The trajectory is too large to share, 59 GB. You are welcome to take a look at it

somehow. Thank you for comments to solve this. I would like to have that

non-pathological 0-200ns trajectory both ways.

Thanks for your time.

Gordon Chalmers
Department of Computer Science
Complex Carbohydrate Research Center
University of Georgia
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Received on Wed May 10 2017 - 06:00:06 PDT
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