[gmx-users] pdb2gmx changes conformation? shch406 at bpci.kiev.ua
Tue Jan 24 19:23:09 CET 2012


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


Thanks in advance,
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