[Chimera-users] PDB column overlap --PDB2PQR,APBS

Nikolay Igorovich Rodionov nirodion at syr.edu
Wed May 16 14:59:17 PDT 2012

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.


Can anyone think of a potential fix? I've experienced this same problem with smaller helix pdb files.

Thank you,
Nikolay Rodionov
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