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?
Cheers,
Veronica
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Received on Fri Aug 05 2016 - 07:30:03 PDT
