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<p class=MsoNormal>Hello Chimera team,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I recently conducted a MD simulation of a 12-mer peptide adjacent
to a hydroxyapatite crystal using NAMD 2.6. When I viewed the output
coordinates from the simulation in pdb format using Chimera 1.4, the protein
ribbon was broken and the hydrogens of certain residues were not bonded but in
close proximity. All of the non-bonded hydrogens were colored purple by
default. The waters of the system and the crystal looked normal. Overall, the
protein looked distorted. I decided to visualize the peptide using VMD 1.8.7 and
to my surprise the protein ribbon was intact with all hydrogens bonded to their
respective residues. Any insight into why this difference occurred would be
greatly appreciated.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Best,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Keith Battle<o:p></o:p></p>
<p class=MsoNormal>Research Technician<o:p></o:p></p>
<p class=MsoNormal>University of South Alabama <o:p></o:p></p>
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