[gmx-users] gmx sasa output group not recognised
teemu.murtola at gmail.com
Fri Sep 4 13:43:14 CEST 2015
The other possibility is that your index groups do not have the atom
indices in an increasing order. If this is the case, just sort the atoms,
or don't use make_ndx as an intermediate step.
On Fri, Sep 4, 2015, 14:20 Francesco Carbone <fra.carbone8 at gmail.com> wrote:
> 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>
> > Hello,
> > On Fri, Sep 4, 2015 at 1:51 PM Francesco Carbone <fra.carbone8 at gmail.com
> > wrote:
> > > 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
> > 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;
> > 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:
> > https://gerrit.gromacs.org/#/c/5050/
> > Best regards,
> > Teemu
> > --
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