[gmx-users] Automatically assign the protonation states for pdb2gmx

[ZHANG Cheng]

I want to run more than 300 MD, each with a different PDB (more precisely, variants derived from a same wild type). I need to manually assign the protonation states using the "-inter" option every time, which is impossible for more than 300 times. 


gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce  -inter  -ignh -merge interactive 


The protonation states come from the pdb2pqr website. Is there an alternative way to obtain the .gro file by providing the necessary inputs (e.g. pdb, protonations), so that I can batch obtain the 300 corresponding .gro files?


I know the "echo" could not work for the charge assignment.


It would be ultimately possible if I can understand the fundamental codes behind "pdb2gmx", then write a batch code to process multiple PDB files at once. But is there a simpler route?