Hi,
My apologies for the extremely late reply on this.
You should make sure you are using an up-to-date version of cpptraj
(version >= 15). I was able to run the tutorial as written with no
errors.
-Dan
On Fri, Aug 5, 2016 at 10:15 AM, Ilkow, Veronica
<veronica.ilkow.kcl.ac.uk> wrote:
>
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Oct 13 2016 - 06:30:02 PDT
