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 - 06:00:03 PST
