[AMBER] Cpptraj-PCA Warning

From: Ilkow, Veronica <veronica.ilkow.kcl.ac.uk>
Date: Fri, 5 Aug 2016 14:15:50 +0000

Dear All,

I am trying to follow the PCA tutorial described here: http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/

I number of warnings turn up when I try to follow the tutorial no matter how I try to edit the trajectory files. The errors are

1)Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.

2)Warning: Parm [X]' selected # atoms (21993) > original parm [Y]'
Warning: selected# atoms (21983).

3)Warning: # atoms in current topology (21993) != # atoms in coords set X-Y-traj" (21983)
Warning: The resulting COORDS data set may have problems.

This leaves me with a trajectory file in which aromatic rings and disulphides are bent out of shape. How can I avoid error 1) and why should error 2 and 3 matter if I have a mask in place which does have the exact same number of atoms?

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Received on Fri Aug 05 2016 - 07:30:03 PDT
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