One of the recurring questions on the list seems to be how to define residue protonation states non-interactively in pdb2gmx input. The interactive options are a bit of a nightmare to use. Could pdb2gmx be modified to optionally read the residue types from the PDB file itself? The user would replace e.g. "ASP " with "ASPH" in the PDB file, and pdb2gmx would build a protonated aspartate, whether the hydrogen atom is there in the PDB file or not. Same for all residue types, of course. The upside would be having readable and more easily scriptable input instead of trying to script the interactive input. I realize that the names of the residue types differ between force fields, but even requiring force field specific names would be ok as far as I'm concerned (ASPH in Gromos, ASH in Amber, etc.).
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