Try this 1 | 13 & a N This will select the group 1 and 13 and all the atom having atom ID N.
On Tue, Jul 11, 2017 at 12:19 PM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello, > I am having problems during creating the indexes for atoms which have same > atom labelling for the two/three different molecules in the system (say > nitrogen atom that is labelled as N in both the molecules). > whn i gave the command:- > gmx make_ndx -f md.gro -o a.ndx > i am getting the prompt as :- > Reading structure file > Going to read 0 old index file(s) > Analysing residue names: > There are: 1 Protein residues > There are: 10 Other residues > There are: 200 Water residues > Analysing Protein... > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > > 0 System : 750 atoms > 1 Protein : 10 atoms > 2 Protein-H : 5 atoms > 3 C-alpha : 1 atoms > 4 Backbone : 3 atoms > 5 MainChain : 3 atoms > 6 MainChain+Cb : 3 atoms > 7 MainChain+H : 6 atoms > 8 SideChain : 4 atoms > 9 SideChain-H : 2 atoms > 10 Prot-Masses : 10 atoms > 11 non-Protein : 890 atoms > 12 Other : 140 atoms > 13 TMAO : 140 atoms > 14 Water : 600 atoms > 15 SOL : 600 atoms > 16 non-Water : 374 atoms > > Here i need say the nitrogen present in protein (1 protein: 10 atoms) index > and the nitrogen's present in tmao (13 TMAO: 140 atoms) in the .ndx > file.ie., > i need the nitrogen present in protein and nitrogen's present in tmao in > the index file.. > How can i get this..?? wht will be the commands for this... i tried with > various commands but in vain.... > > > Thank you... > > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > > > > <https://mailtrack.io/> Sent with Mailtrack > <https://mailtrack.io/install?source=signature&lang=en& > referral=cy16f01.di...@nitk.edu.in&idSignature=22> > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.