[gmx-users] Generating a PQR file

[Bob Johnson]

Hello everyone,
I would like to create a PQR file (basically a PDB file but with charges in
B-field and radii in occupancy field). However, there doesn't seem to be any
straightforward way to do this.

I noticed that this could be done with editconf, however this is difficult given
the way I have my topologies set up. I have a separate topology (.itp) for each
molecule in my system (dna, water, counterions, etc.). Thus, the atom numbers
in these files are not unique. Thus, there is no good way of feeding in the
charges to editconf by listing the charge for each atom number. Is there a way
to extract this information from a .tpr file?
Thanks,
Bob Johnson