I am trying to get coordinates for the vector normal to the plane of the 6 ring atoms of uracil.
In both ptraj and cpptraj I do not get an output file and I get the message:
Warning: Output of corr, ired, corrired or corrplane vectors is not yet supported!
Is there a work around for this?
Note when I use the syntax given in AmberTools13:
vector corr plane :6.N1.C2,N3,C4,C5,C6 out U6_plane.vec
I get the following error:
wrong syntax: o
parsing atom mask: unknown symbol (?)
Segmentation fault
However when I use the old syntax from AmberTools
vector v01 :6.N1,C2,N3,C4,C5,C6 corrplane out U6_plane.vec
Both ptraj and cpptraj execute and report progress to the standard output, but both fail to produce the output file.
I am using AMBER13. My trajectory has had all but the closest 1500 water removed. I used RDPARM to generate the topology file for the reduced water frames.
Mike Bruist
University of the Sciences
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Received on Thu Feb 27 2014 - 12:00:04 PST
