Hi all, 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? 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. http://dl.dropbox.com/u/42179401/2TMV.18H.pdb http://dl.dropbox.com/u/42179401/2TMV.18Ha.pqr Can anyone think of a potential fix? I've experienced this same problem with smaller helix pdb files. Thank you, Nikolay Rodionov