[gmx-users] using do_dssp secondary structural analysis, beta-sheet issues

[Nagaraju Mulpuri]

Dear All,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):residue number    1   2   3    4   5 ......10coil                       0.1 0.1 0.1 0.1 0.1 .... 0.1helix                     0.1 0.1 0.1 0.1 0.1 .... 0.1sheet                   0.1 0.1 0.1 0.1 0.1 .... 0.1I  am trying to use the following command to do secondary structural analysis:gmx do_dssp -f protein.xtc -s protein.gro -n protein.ndx -o chain_1.xpm -tu ns -sc chain_scount.xvg cmx xpm2ps -f chain_1.xpm -o chain_1.psWhen I run above commands on single chain, beta sheets were not shown (chain_1.ps), but when I ru
 n on all chains (10 chains) it is showing existence of beta sheets. At the end of chain_scount.xvg (when using -sc option) file, commented line(# SS%), does it represents percentage of secondary structure?Any help or suggestions is appreciated.Thank you very much.Sincerely,Nagaraju