[gmx-developers] pdb2gmx

[Ran Friedman]

Anton Feenstra wrote:
> Doesn't pdb2gmx check for an (optimal?) H-bonding network for ASP and
> GLU protonation?
I don't think so.
> Otherwise IMHO the issue is moot, since the group is rotatable, so
> both oxygens are interchangable in the structure (and will swap during
> simulation).
This is indeed often the case in MD simulations. However, neutron
diffraction structures sometimes show a preferable protonation state and
there must be a reason for that.

Best,
Ran.