[gmx-users] gmx sasa output group not recognised
fra.carbone8 at gmail.com
Fri Sep 4 13:20:42 CEST 2015
thank you for the reply, but the residues are in the same protein.
I simply select a list of residues that interact with the substrate.
(echo "r 171 263 201 202 205 395 365 239 360 258"; echo "name 10 G6P"; echo
"q") | make_ndx -f $nameprod.gro -o $name1.ndx
residues 171 263 201 202 205 395 365 239 360 258 are part of "Protein".
On 4 September 2015 at 12:12, Teemu Murtola <teemu.murtola at gmail.com> wrote:
> 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
> > 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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