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.
