Dear Thomas E. Cheatham, III
> > i have an error message when running ptraj using
> > amber8. it seems that ptraj cannot read my crd
> files..
> > can somebody help me to solve this problem? when i
> > look at the 1jkmpro3.out i found that there is a
> > message :
> >
> > check COM velocity, temp: 0.002752
> > 0.01(Removed)
> >
> >
> > Unit 16 Error on OPEN: 1jkmpro3.xyz
>
> The above is not an error from ptraj, but likely
> sander and states that
> the file "1jkmpro3.xyz" could not be opened.
> Perhaps that file already
> exists (zero sized) or write permission is not
> granted?
yes this is not an error from ptraj but from
1jkmpro3.out. i've the permission and i dont know why
this happen and suddenly it stop the calculation.
> > Could not open file (1jkmpro3.crd) with mode (r)
> > WARNING in checkCoordinates(): Could not open file
> > (1jkmpro3.crd)
> > WARNING in ptrajSetupIO(): trajin 1jkmpro3.crd,
> cannot
> > open file...
>
> ptraj will only complain like this is the file
> actually does not exist.
when i do head 1jkmpro3.crd.. and the output is this:
42.117 30.815 65.329 41.870 30.110 66.008 42.346
31.652 65.845 42.959 30.429 64.925 41.130
31.065 64.306 41.545 31.773 63.589 40.727 29.760
63.627 40.346 29.076 64.385 39.945 30.026
62.917 41.949 29.216 62.859 42.767 28.069 63.271
42.465 27.507 64.143 43.921 27.678 62.594
44.503 26.867 63.006 44.165 28.238 61.351 45.317
27.974 60.670 45.815 27.196 60.933 43.422
29.381 60.972 43.728 29.811 60.030 42.371 29.870
61.756 41.705 30.642 61.400 39.906 31.761
64.900 39.630 31.582 66.068 39.147 32.519 64.164
39.481 32.765 63.243 37.986 33.280 64.638
37.612 32.804 65.545 38.413 34.750 65.032 37.530
35.271 65.401 39.137 34.716 65.8
> Do a "ls" in your current directory and see if
> 1jkmpro3.crd is actually
> there (or type "head 1jkmpro3.crd").
i do ls and i found there is a file 1jkmpro3.crd but
when i try to vi 1jkmpro3.crd the computer become
"hang" ...
by the way thanks for your reply
Abd Ghani
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Received on Fri Nov 05 2004 - 02:53:00 PST
