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

Zhang, Cheng c.zhang.11 at ucl.ac.uk
Thu May 21 16:38:51 CEST 2015

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


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