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 - 11:30:03 PST
