Hi, I applied pdb2gmx to PDB file A.pdb with force field gromos53a5 and water model spc and then compared the resulting A.gro file with initial PDB one, using program g_rmsdist by the following command: /opt/software/gromacs/gromacs-4.5.3-intel/bin/g_rmsdist -f A.gro -s /home/shch406/PDB/A.pdb -o A.dA.xvg
Structures appeared to be quite different - RMSD = 1.67! @ subtitle "of distances between Protein atoms" 0 1.67265 Why? Thanks in advance, Igor
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