[gmx-users] pdb2gmx changes conformation?

[192.168.100.1]

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  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120124/185e439c/attachment.html>