<p>Hi Igor,</p>
<p>Please look at the contents of the files. Note the order of atoms.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Jan 24, 2012 7:31 PM, "192.168.100.1" <<a href="mailto:shch406@bpci.kiev.ua">shch406@bpci.kiev.ua</a>> wrote:<br><br><u></u>
<div bgcolor="#ffffff">
<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></div>
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