[gmx-users] Protein surface interaction analysis - hydrophobic sasa

[Milan Sobota]

Dear gromacs users,

I am simulating the binding of a peptide to a hydrophobic polymer surface
(100 short polymer chains arranged in a brush like layer). I want to
calculate the hydrophobic and hydrophilic sasa seperately, as well as the
contact area, which should be the decrease in hydrophobic sasa upon
binding. To do this, I ran:
gmx sasa -surface 'group "non-Water"' -output '"Hydrophobic" group
"non-Water" and charge {-0.2 to 0.2}; "Hydrophilic" group "Protein" and not
charge {-0.2 to 0.2}; "Total" group "Protein"'
as described at
http://manual.gromacs.org/documentation/2016.3/user-guide/cmdline.html#g-sas

Is this the right approach, or what would be the right one? Does this count
the hydrophobic contact area twice for my case, since I have more than just
protein in the "non-water" group?

Additionally, I am using g_mmpbsa and gmx mindist to calculate binding
energies and contact timelines. Are there other ways to analyze this type
of interaction that I should be aware of?

Thanks and kind regards,

Milan H B Sobota
RWTH Aachen University