{% extends "layout.html" %} {% block title %}Add Hydrogens and Water{% endblock %} {% block body %}

Add Missing Hydrogens

PDB files often do not include hydrogen atoms. Do you want to add missing hydrogens? The set of hydrogens that gets added will depend on what pH you want to simulate the system at.

Add Water/Membrane

Add a water box or membrane surrounding the model?

How do you want to select the size of the water box?


{% if unitCell is not none %}
{{ '%.3f' % unitCell[0] }}
{{ '%.3f' % unitCell[1] }}
{{ '%.3f' % unitCell[2] }}
{% endif %}
{{ '%.3f' % boundingBox[0] }}
{{ '%.3f' % boundingBox[1] }}
{{ '%.3f' % boundingBox[2] }}
The largest dimension of the model (along the x, y, or z axis) will be determined, and the specified padding will be added to each edge of the box.
The membrane will lie in the XY plane and be centered at Z=0. Make sure the protein is properly oriented and positioned. When possible, it is easiest to use a PDB file from OPM since they are already properly positioned.

Ions will be added to neutralize the model. You can optionally add more ions based on a desired bulk ionic strength.

{% endblock %}