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

[Justin Lemkul]

On 1/21/20 8:17 PM, Nagaraju Mulpuri wrote:
> 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

If a sheet is composed of multiple chains, you have to include all 
relevant chains in the analysis. DSSP defines secondary structure based 
on hydrogen bonding patterns. If there is no second chain with which the 
first interacts to form a sheet, then DSSP says no sheet exists at all.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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