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

Mark Abraham mark.j.abraham at gmail.com
Wed Jul 25 21:34:14 CEST 2018


Which groups Sasa are you trying to measure?


On Wed, Jul 25, 2018, 12:16 Milan Sobota <milanh.b.sobota at gmail.com> wrote:

> 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
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