Hi priya <br><br><a href="http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx" target="_blank">http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx</a> these <br>link may be help to you <br><br>i like to know how to calculate index groups for my micelles..<br>
<br>since
i am having two micelles , one having 8molecules and another having
2molecules.. residue number for that 2molecule micelle is 2 and 7..<br>
<br>can you help me how to form index group for this two micelles..<br><br>make_ndx command need to be used .<br><br>i searched but couldnt get the point clearly ..<br><br>make_ndx –f .....gro/pdb –o my_index.ndx<br>You will see the following output (we left out the descriptive info at the beginning) followed by acommand prompt (>).<br>
<br>Reading structure file<br>Going to read 0 old index file(s)<br>Analysing residue names:<br>There are: 129 Protein residues<br>There are: 10824 Water residues<br>There are: 8 Ion residues<br>Analysing Protein...<br>
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<br><br> 0 System : 34440 atoms<br> 1 Protein : 1960 atoms<br> 2 Protein-H : 1001 atoms<br> 3 C-alpha : 129 atoms<br>
4 Backbone : 387 atoms<br> 5 MainChain : 517 atoms<br> 6 MainChain+Cb : 634 atoms<br> 7 MainChain+H : 646 atoms<br> 8 SideChain : 1314 atoms<br> 9 SideChain-H : 484 atoms<br>
10 Prot-Masses : 1960 atoms<br> 11 non-Protein : 32480 atoms<br> 12 Water : 32472 atoms<br> 13 SOL : 32472 atoms<br> 14 non-Water : 1968 atoms<br> 15 Ion : 8 atoms<br>
16 CL : 8 atoms<br> 17 Water_and_ions : 32480 atoms<br><br> nr : group ! 'name' nr name 'splitch' nr Enter: list groups<br> 'a': atom & 'del' nr 'splitres' nr 'l': list residues<br>
't': atom type | 'keep' nr 'splitat' nr 'h': help<br> 'r': residue 'res' nr 'chain' char<br> "name": group 'case': case sensitive 'q': save and quit<br>
'ri': residue index<br><br>> <br><br>Use the ‘r’ command to enter the list of residue numbers that represent the N & C termini of the<br>triple helix.<br>> r 1 36 37 72 73 108<br>15 r_1_36_37_72_73_108 :<br>
51 atoms<br>Note: You may also use a dash to specify a residue number range (e.g. to specify residues 1 to 36<br>use > r 1-36) ... OR, better yet, lets specify a residue range only including backbone atoms. Do<br>this with the ampersand for example ...<br>
> r 1-36 & a C N CA<br>The default name (r_1_36_37_72_73_108 ) giving to the new index group that you have just<br>created is cumbersome. Lets rename it using the name command. We will use the index group #<br>(15) in the command.<br>
> name 15 Terminal<br>> v(Verbose)<br>>h for help give information on index tool <br>>q for quite..<br>And use these index file by specifying it for further analysis...<br><br><br>you can make group by specifying atom no 0r range of atom that form micelle ..<br>
<br><br>Have a nice day........<br>With Best Wishes,<br><br><br>