as per your suggestion i have tried the command
"*head fimd.mdcrd*"
and the output is as follows.
40.503 43.599 83.584 41.273 42.427 83.174 40.850 42.018 82.272
42.245
42.794 82.890 41.339 41.274 84.192 41.875 41.570 85.078 40.027
40.806
84.606 39.882 39.367 84.514 39.649 38.906 85.451 38.981 38.991
83.375
38.577 39.769 82.381 38.760 40.823 82.339 37.901 39.200 81.498
37.904
37.919 81.823 37.357 36.748 81.182 36.658 36.768 80.215 37.580
35.564
81.904 37.092 34.743 81.575 38.257 35.480 83.046 38.391 34.265
83.590
37.903 33.524 83.106 38.914 34.092 84.436 38.805 36.511 83.688
38.587
37.723 83.015 42.005 40.050 83.538 41.823 39.972 82.479 41.299
38.865
84.178 41.289 37.955 83.603 41.857 38.522 85.492 42.775 38.248
85.424
and as per your second suggestion to leave out the spaces in the atom
selection mask, and the final comma
after O3' has no impact on the error.
sir, plz help me in solving the error.
---------- Forwarded message ----------
From: case <case.biomaps.rutgers.edu>
Date: Tue, Dec 27, 2011 at 7:12 PM
Subject: Re: [AMBER] Fwd: Fwd: WARNING in ptraj(): No input trajectories
specified (trajin), aborting...
To: AMBER Mailing List <amber.ambermd.org>
On Tue, Dec 27, 2011, rosy stone wrote:
> input file is as follows
> *
> *trajin fimd.mdcrd*
> *rms first mass out m22g_calc_backbone.rms .P,O5', C5', C4', C3', O3',
time
> 0.2.*
>
> the input trajectory is in the same folder where i am running the ptraj
> command.
>
For some reason, ptraj doesn't agree:
> > PTRAJ: trajin fimd.mdcrd
> >
> > Checking coordinates: fimd.mdcrd
> > trajin fimd.mdcrd ignored; could not open file (fimd.mdcrd)
Make sure you have read permission for the fimd.mdcrd. Try the command
"head
fimd.mdcrd" to see if you can indeed read it, and that it looks like other
trajectory files that "work".
Also, leave out the spaces in the atom selection mask, and the final comma
(after O3'):
rms first mass out m22g_calc_backbone.rms ".P,O5',C5',C4',C3',O3'" time 0.2.
....dac
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Received on Tue Dec 27 2011 - 21:30:02 PST
