[gmx-users] Solvent Accessible Surface Area (SASA): Separate Hydrophobic and Hydrophilic components

Nuria Codina nuria.codina.15 at ucl.ac.uk
Wed Jul 12 17:15:01 CEST 2017


I want to measure the Hydrophobic and Hydrophilic components of the Solvent
Accessible Surface Area. In the Tool Changes for 5.0 I found these command:

gmx sasa -s md.tpr -f md_traj.trr -surface 'group "A"' -output
'"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B"
and not charge {-0.2 to 0.2}; "Total" group "B"'

And I tried changing "A" and "B" for "protein", but it is not working for
me. Could you show me an specific example that worked for you?

Thanks very much,

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