[gmx-users] Regarding Secondary Structure Analysis

Nagaraju Mulpuri mulpurinagaraju at rediffmail.com
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):               residue number: 1       2      3     4     5     6     7     8     9     10               coil:                     0.1     0.1    0.1    0.1    0.1    0.1    0.1    0.1                helix:        
            0.1    0.1    0.1    0.1    0.1    0.1    0.1    0.1               B-sheet:               0.1    0.1    0.1    0.1    0.1    0.1    0.1    0.1               I am trying to use the following command to do secondary structural analysis: gmx do_dssp -f protein.xtc -s protein.gro -n chain_1.ndx -o chain_1.xpm -tu ns -sc chain_scount.xvg​gmx 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 run on all chains (10 chains) it is showing existence of beta sheets (protein.ps file).  At the end of chain_scount.xvg (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? Any help or suggestions are appreciated.Thank you very much.Sincerely,Nagaraju


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