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superimposing_residues_from_a_trajectory_using_cpptraj

Superimposing residues from a trajectory using cpptraj

Execute the following input file (e.g. trajin.in) using cpptraj to generate the multiPDB hairpin.MD.pdb.

cpptraj -p hairpin.top < trajin.in

trajin hairpin.md1.rst.bz2
trajin hairpin.md500.rst.bz2
trajin hairpin.md1000.rst.bz2
trajin hairpin.md1500.rst.bz2
trajin hairpin.md2000.rst.bz2
trajin hairpin.md2500.rst.bz2
trajin hairpin.md3000.rst.bz2
reference hairpin.crd
rms reference :6-9,31-34
center :6-9,31-34 mass origin
image origin center familiar
strip :WAT,Na,Cl
trajout hairpin.MD.pdb
go

superimposing_residues_from_a_trajectory_using_cpptraj.txt · Last modified: 2016/07/27 15:32 by root