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