Dear AMBER users
I have a protein-protein complex. The first protein is a homodimer and I
planned to calculate the RMSD for each subunit to the experimental pdb file
as reference. Of course, the number of amino acid residues in pdb have
numbering differs from numbering in complex and the recipe I used
parm complex_dry.prmtop
trajin complex_dry.nc
parm 2R_dimer.pdb
reference 2R_dimer.pdb parm 2R_dimer.pdb [2R]
rms To2R ref [2R] ":.A:69-150.CA" ":.B.CA:185-266&!(.H=)" nofit mass out
complex_RMSD_LIG_nofit_1.dat
I got Error: No reference atoms selected for parm 2R_dimer.pdb.
Thank you in advance
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Received on Sat May 10 2025 - 12:30:02 PDT
