Atom name mapping between lib and pdb files

[wxx07]

Hi modXNA developers,

Thank you for creating this helpful tool!

I have a question regarding the generated library (lib) file. When using tleap to create AMBER topology and coordinate files, we will load an external PDB file containing modified nucleotides. Do the atom names of the modified nucleotides in the PDB file need to exactly match those in the generated lib file?

If a match is required, is there an automatic way to handle this mapping, or must it be done manually (e.g., in a text editor)?

Thank you for your guidance!

[drroe]

Hi,

LEaP requires that incoming atom names match the atom names in whatever template (library file) you have loaded, but the ordering does not matter. As far as I know, modXNA uses standard PDB atom names (like the rest of Amber), so hopefully there should not be any mismatches. If your PDB has non-standard atom naming you may be able to use the atommap changenames functionality of CPPTRAJ to change the names to the ones expected in the template.

Pinging @cbergonzo and @rodrigogalindo so they see this.

[wxx07]

Thank you for your quick response! That is exactly what I need since I find that PDB outputed by OpenBabel or Pymol often has non-standard atom naming for engineered residues. Thanks!