[gmx-users] Regarding creating indexing with atoms having same labelling in different molecules
mark.j.abraham at gmail.com
Tue Jul 11 09:19:25 CEST 2017
That is, Tasneem's recipe will find all atoms that are in group 1 OR group
13, AND whose name is N. If Dilip just wants the atoms in group 1 AND whose
name is N, then e.g.
1 & a N
There are some examples in the interactive help of gmx make_ndx
On Tue, Jul 11, 2017 at 9:14 AM Tasneem Kausar <tasneemkausar12 at gmail.com>
> 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.dilip at nitk.edu.in>
> > Hello,
> > I am having problems during creating the indexes for atoms which have
> > 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)
> > 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
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> > referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
> > --
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