[gmx-users] pdb2gmx: can we use a file to specify the protonation instead of using "-inter"?

[Zhang, Cheng]

Dear GROMACS experts,

Can I ask is there a more efficient way to deal with the "-inter" option in the pdb2gmx command?


Now, I have to manually assign individual protonation status one by one, which takes a very long time. Sometimes I make a mistake and I have to re-do all of them again.


Would it be possible if the command line can link to a file, which specifies the protonation for individual residues?


Thank you very much.


Yours sincerely

Cheng