[gmx-users] Doubt about correct system preparation sequence when protonation state calculation and ligand presence are involved

[Gustavo Avelar Molina]

Hi everyone,

I'm a little confused about the most correct sequence of the minimization,
equilibration, solvatation and neutralization steps when I need to simulate
a protein in a specific pH (through the protonation state calculation in
this pH by using H++, for instance) and/or place a ligand in this protein (be
it through covalent bonding or not). For instance, I've seen papers in
which people use the following sequence: minimization, solvatation, H++
calculation, neutralization and equilibration, which is not so intuitive to
me. Moreover, I've noticed that the sequence affects substantially the
resulting protonation state in H++, but not so much the pI.

So, I would like to know what is the most appropriate system preparation
sequence for a protein simulation when I need it with the protonated state
corresponding to a certain pH and when I need to place a certain ligand in
this protein.

I would be very grateful if someone could explain it me.

Regards,

Gustavo