Hi,
i use g_rms to calculate rms,
as reference structure (-s) i use myprotein.pdb file
and trajectory (-f) is a trajectiry after MD MDprotein.pdb.
The thing is that myprotein.pdb and MDprotein.pdb have the same atoms BUT
their order within a residue is DIFFERENT.
example:
myprotein.pdb:
ATOM 1 N ALA E 1 18.858 -22.883 26.306 1.00 0.00
ATOM 2 CA ALA E 1 19.106 -24.277 26.027 1.00 0.00
ATOM 3 C ALA E 1 20.206 -24.458 25.006 1.00 0.00
ATOM 4 O ALA E 1 20.156 -23.801 23.972 1.00 0.00
ATOM 5 CB ALA E 1 17.865 -24.819 25.301 1.00 0.00
MDprotein.pdb:
ATOM 1 N ALA 1 18.861 24.179 26.290 1.00 0.00
ATOM 2 CA ALA 1 18.978 22.741 26.011 1.00 0.00
ATOM 3 CB ALA 1 17.670 22.190 25.440 1.00 0.00
ATOM 4 C ALA 1 20.069 22.592 24.949 1.00 0.00
ATOM 5 O ALA 1 20.120 23.450 24.070 1.00 0.00
whether g_rms work correct in this case?
g_rms -s myprotein.pdb -f MDprotein.pdb
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