On 8/8/23 9:43 AM, sedmo.info--- via modeller_usage wrote: > I have used modeller to generate a pdb file. unfortunately, the pdb > file is not regular as the columns 10 and 11 interfere. What can I > do? I can not use the pdb file to generate a psf file.

Can you be a bit more specific? Perhaps show part of the problematic PDB file. Modeller should generate conformant PDB files. I'm not sure what you mean by "columns 10 and 11 interfere". If you're talking about the ATOM records those should just be part of the serial number: https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#...

BTW, Modeller can generate PSF files itself: https://salilab.org/modeller/10.4/manual/node187.html

Ben Webb, Modeller Caretaker