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<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am trying do Poisson-Boltzmann calculations through outside software, PDB2PQR and APBS. I am prepare my initial pdb file in chimera using the ‘write pdb’ method. The final structure is quite large, 737058 atoms, so I am getting overlaps
in the data columns after I write the PDB file. This doesn’t create a problem for rendering the PDB file but I get parsing errors and other strange occurrences when I try to create a complementary PQR file. Does anyone know of a work around?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here are links to my structures, if you look you will see that a significant portion of the structure is getting cut off in the PQR. I can’t seem to generate more than about 99760 atoms, no matter what I try.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">http://dl.dropbox.com/u/42179401/2TMV.18H.pdb<o:p></o:p></p>
<p class="MsoNormal">http://dl.dropbox.com/u/42179401/2TMV.18Ha.pqr<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Can anyone think of a potential fix? I’ve experienced this same problem with smaller helix pdb files.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you,<o:p></o:p></p>
<p class="MsoNormal">Nikolay Rodionov<o:p></o:p></p>
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