[gmx-users] gmx sasa output group not recognised

Teemu Murtola teemu.murtola at gmail.com
Fri Sep 4 13:12:49 CEST 2015


On Fri, Sep 4, 2015 at 1:51 PM Francesco Carbone <fra.carbone8 at gmail.com>

> I've recently started using gromacs 5.0.4 and I can't make"gmx sasa" to
> recognise non-standard groups for the -output flag.
> I have three groups (G6P, Co-enzyme and strNADP+; all subset of the dimer )
> and every time I specify one of the three with "-output" flag I get:
> "Inconsistency in user input: Output selection is not a subset of the input
> selection ".
> I created the groups with make_ndx and "gmx sasa" see them correctly
> (option 10,11 and 12) and these are the commands that I tried:
> 1) gmx sasa -s Ameno_500.tpr -f Ameno_500.xtc -n Ameno.ndx -surface
> "Protein" -output "G6P" -o ciao.xvg -dt 250

Most likely, your G6P group is not a subset of the Protein group (which is
very likely if you have some non-standard residues or such). As mentioned
in 'gmx sasa -h', the group specified for -output should be a subset of
what is specified for -surface. There was no such check in g_sas in 4.6; it
just ignored any atoms in the output group that were not in the surface
group, which in my mind is worse (since that almost always means that the
user is not computing what they think they are).

I improved the error message to include more information here:

Best regards,

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