[gmx-users] g_rms

[Tatsiana Kirys]

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