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Hello Klara--
>
> Thank you very much for the prompt response. I put a file named m341.tar
> on the ftp site - please let me know if there is any problem with the
> file. It contains the following:
>
I figured out the problem with your files: the axis atoms do not
define an orthogonal coordinate system. Using the orthogonalized
coordinates:
ATOM 2440 X ANI 500 0.489 -7.608 -6.902 1.00 0.00
ATOM 2441 Y ANI 500 0.479 -6.591 -7.884 1.00 0.00
ATOM 2442 Z ANI 500 0.902 -7.898 -8.223 1.00 0.00
ATOM 2443 OO ANI 500 1.166 -7.226 -7.531 1.00 0.00
I find that vmd-xplor and the SANI term agree well. Here are the
results for the first few residues
SANI VMD-XPLOR
8 GLU HN 8 GLU N -18.682 -18.684
9 LEU HN 9 LEU N 6.192 6.18938
11 VAL HN 11 VAL N 7.440 7.43588
12 ALA HN 12 ALA N 8.758 8.7578
13 VAL HN 13 VAL N 18.308 18.3081
14 GLU HN 14 GLU N 16.207 16.2066
15 THR HN 15 THR N 10.320 10.3172
16 LEU HN 16 LEU N 7.267 7.26662
17 ALA HN 17 ALA N 18.766 18.7661
I'm not sure how your axis got so torqued- maybe running with an
exceptionally high temperature. An alternative would be to use the IVM
in either the XPLOR or Python interfaces. With that, you can specify
that the axes never deviate from orthogonality. Please see
eginputs/protG for simple examples.
regards--
Charles
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