Development suggestion: Option to choose histidine tautomers/charge

[KasperBuskPedersen]

Hi

First of all, thank you for developing this amazing tool.

Would it be possible to implement an option to choose (either interactively or specifying in a file) histidine tautomers per histidine for the backmapped AA structure? I see that you already use pdb2gmx, so maybe it could be quite easily done using -ignh and -his? This will save some post-processing of the output and make the NVT quilibration more accurate

Maybe there is a clever way to do this using the -swap command, however the database doesn't seem to include histidine tautomer fragments

Thank you in advance Kasper

[owenvickery]

Hi,

It is easier to add the fragments and use the swap command. I'll add the HIS tautomers to the fragments when I have time.

pdb2gmx is very clunky and you have to know in advance how many his residues there are and which one you want to change.

Plus it overrides pdb2gmx automated HIS optimiser to select the best His tautomer, which forces you to then identify the best for each His residue yourself.

That and the order of the selections changes depending on forcefield.

I've yet to find a good way around pdb2gmx.