Dear Dr. Thomas,
Regards. I'm glad and thankful for your kind
explanation and I'm taking your advise to do a
"checkoverlap" to check for oo close contacts.
However, I'm facing some technical problem now as I do
not know how should I understand the output file.
I've tried several ptraj scripts to trajout an output
(or no trajout), but it just couldn't work. If I
trajout an output, what should be the format of the
output file? If I don't put the trajout command, there
will be no output (obviously), and how am I going to
check then?
Example ptraj script that does trajout:
trajin rst
trajout out
checkoverlap noimage
go
$ptraj prmtop <script> logfile
I checked the out file (where ptraj assumes it's a
trajectory file, default..I know), logfile (not much
information). Out file has output like this:
rdparm transformed trajectory
7.103 50.209 127.770 6.339 49.655 127.522
6.761 48.308 127.373 7.367
48.212 126.471 5.884 47.667 127.279 7.577
47.859 128.588 7.031 48.099
129.501 7.853 46.461 128.574 9.173 46.258
129.087 9.179 45.566 129.930
10.052 45.715 128.021 9.810 45.621 126.673
8.914 46.013 126.215 10.733
44.992 126.000 11.693 44.673 126.972 12.950
43.970 126.890 13.507 43.459
125.919 13.585 43.840 128.110 14.441 43.310
128.129 13.078 44.301 129.276
13.758 44.055 130.362 14.612 43.500 130.325
13.374 44.392 131.219 11.930
44.963 129.404 11.278 45.118 128.211 8.927
48.563 128.645 9.382 48.554
<file truncanted>
How to analyse these information?? Any ideas?? Please
advise. Thanks a lot.
Regards,
Yam
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Received on Fri Jul 29 2005 - 03:53:00 PDT
