[gmx-users] Regarding Secondary Structure Analysis

Tue Jan 21 09:58:08 CET 2020

Dear Gromacs Users,I am trying to analyse secondary structure of protein. The trajectory generated using Gromacs and protein contains 10 chains. I want to know secondary structural changes, occupancy of each residue in each chain.example (sum on whole trajectory of a chain or protein):&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; residue number: 1 &nbsp; &nbsp;&nbsp;&nbsp;&nbsp;2&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;3&nbsp;&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp; 6&nbsp;&nbsp;&nbsp;&nbsp; 7&nbsp;&nbsp;&nbsp;&nbsp; 8&nbsp;&nbsp;&nbsp;&nbsp; 9&nbsp;&nbsp;&nbsp;&nbsp; 10&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;coil: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.1&nbsp;&nbsp;&nbsp;&nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp;helix:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; B-sheet:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp; &nbsp; 0.1&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;I am trying to use the following command to do secondary structural analysis:&nbsp;gmx do_dssp -f protein.xtc -s protein.gro -n chain_1.ndx -o chain_1.xpm -tu ns -sc chain_scount.xvggmx xpm2ps -f chain_1.xpm -o chain_1.psWhen I run above &nbsp;commands on single chain, beta sheets were not shown(chain_1.ps), but when I run on all chains (10 chains) it is showing existence of beta sheets (protein.ps file).&nbsp;&nbsp;At the end of&nbsp;chain_scount.xvg&nbsp;(when using 
 -sc option) file, commented line (# SS %), does it represent percentage of secondary structure?what is meant by chain_separator in legends in scount.xvg file?&nbsp;Any help or suggestions are appreciated.Thank you very much.Sincerely,Nagaraju