[gmx-users] Solvent Accessible Surface Area (SASA): Separate Hydrophobic and Hydrophilic components
Hi,
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,
Núria
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[gmx-users] Gromacs 5.0 - Solvent Accessible Surface Area (sasa) separate Hydrophobic and Hydrophilic components
Hi,
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,
Núria
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