GROMACS version:
GROMACS modification: Yes/No
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Hello, I have successfully run all the gromacs commands excluidng the calculation of hydrophobic and hydrophilic area by SASA. I understand that it needs to be specified by the -surface selection. I have followed the manual and wrote like this:
SASA
echo 1 | singularity run --no-home -B ${PWD} --nv ./gromacs_2018.2.sif gmx sasa -f md_fit_380.xtc -s md_380.tpr -o sasa_Hydrophobe.xvg -surface ‘group “A”’ -output ‘“Hydrophobic” group “A” and charge {-0.2 to 0.2};“Hydrophilic” group “A” and not charge {-0.2 to 0.2}’ -tu ns
However I keep getting this error:
Error in user input:
Invalid command-line options
In command-line option -surface
Invalid selection ‘group’
Near ‘group’
syntax error
In command-line option -output
Invalid selection ‘group’
Near ‘group’
syntax error
In command-line option -output
Invalid selection ‘and’
Near ‘and’
syntax error
In command-line option -output
Invalid selection ‘charge’
Near ‘charge’
syntax error
In command-line option -output
Invalid selection ‘{-0.2’
Near ‘{’
syntax error
In command-line option -output
Invalid selection ‘to’
Near ‘to’
syntax error
In command-line option -output
Invalid selection ‘0.2}’
Near ‘}’
syntax error
In command-line option -output
Invalid selection ‘group’
Near ‘group’
syntax error
In command-line option -output
Invalid selection ‘and’
Near ‘and’