[gmx-users] Gromacs 5.0 - Solvent Accessible Surface Area (sasa) separate Hydrophobic and Hydrophilic components

Nuria Codina nuria.codina.15 at ucl.ac.uk
Wed Jul 5 14:01:26 CEST 2017


I would like 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"'

But I get this error:

Error: Multiple groups 'A' selected

Inconsistency in user input:
Invalid index group reference(s)
  Cannot match 'group "A"', because no such index group can be found.

Can you let me know how to define the selection?
I've tried "group 1" and "group protein" as well, but it doesn't recognize
it either.

Many thanks in advance,

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