[gmx-users] minimisation with protonated residues

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Thu Sep 6 15:38:26 CEST 2012

Hi everybody,
I want to do a minimization of the phosphate I added to my protein. I know
that it is protonated once. But I don't know at which position.
How can I handle this with gromacs? Can I somehow "tell" gromacs that this
phosphate is protonated once? Or shell I just protonate it at on position
and run the minimization, protonate it at another position and run the
minimization again?

Thank you,

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