Yun, did you type "go" after defining "trajin" and "trajout"?
Jan-Philip
On 13.11.2011 20:06, Yun Shi wrote:
> Hello all,
>
> This question might be dumb.
>
> But I did MD simulation with other softwares, and used VMD to convert the
> trajectories to dcd format. Now I want to convert it to mdcrd format so
> that I could use MM/PBSA.py within AmberTools to calculate binding
> affinity. But ptraj did not output anything, what I did is:
>
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 11.0 integrated" (4/2010)
> -/- Executable is: "ptraj"
> /-\ Running on 1 processor(s)
> \-/ Input the name of an AMBER prmtop, CHARMM PSF or PDB file:
> npt4382.pdb
> Opened file "npt4382.pdb" with mode (r)
> Reading PDB file "npt4382.pdb": 4382 atoms found!!!
> Found 424 residues
>
> PTRAJ: Processing input from "STDIN" ...
> trajin beta100.dcd 1 1000 1
>
> PTRAJ: trajin beta100.dcd 1 1000 1
> Checking coordinates: beta100.dcd
> trajout beta100.mdcrd mdcrd
>
> PTRAJ: trajout beta100.mdcrd mdcrd
>
>
> And I do not even know how to correctly exit this program (I used "Ctrl +
> C").
>
> Thanks for any suggestion.
> Yun
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Received on Sun Nov 13 2011 - 13:00:04 PST
