[gmx-users] Secondary Structure Analysis using do_dssp

Tue Jan 21 11:13:21 CET 2020

Dear Gromacs Users,&nbsp;I am trying to analyze 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.&nbsp;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;&nbsp;I am trying to use the following command to do secondary structural analysis:&nbsp;&nbsp;gmx do_dssp -f protein.xtc -s protein.gro -n chain_1.ndx -o chain_1.xpm -tu ns -sc chain_scount.xvg&nbsp;gmx xpm2ps -f chain_1.xpm -o chain_1.ps&nbsp;When 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;&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?&nbsp;what is meant by chain_separator in legends in scount.xvg file?&nbsp;&nbsp;Any help or suggestions is appreciated.&nbsp;Thank you very much.&nbsp;Sincerely,Nagaraju&nbsp;