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". Cheers, Francesco On 4 September 2015 at 12:12, Teemu Murtola <[email protected]> wrote: > Hello, > > On Fri, Sep 4, 2015 at 1:51 PM Francesco Carbone <[email protected]> > 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 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: > https://gerrit.gromacs.org/#/c/5050/ > > Best regards, > Teemu > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
