[gmx-users] about using do_dssp for a few residues

[Xu, Jianqing]

Dear all,

I was playing "do_dssp" command in the last a few days.

If I want to know the secondary structures of all the residues on the protein over the trajectory, everything seems good! However, the obtained picture (ss.xpm->ss.eps) is obviously too colourful, as all the residues are shown on there. Somehow, for my project, I am actually only interested in watching a few key residues.

I therefore used the index file to select a few residues that I am interested, and do the same analysis using "do_dssp -s md.tpr -f md.pdb -n index.ndx". I found the secondary structure of the selected residues are always in "Coil" status, which is not consistent with the results obtained by checking the entire protein.

I then did the tests to select 1-10 residues, 1-100 residues and 1-200 residues, and the results were different. The only reasonable possibility that I can think of is that the "do_dssp" only checks the selected residues and assumes the rest of the protein do not exist ....

I was wondering whether my understanding is correct. And if this is the case, how can I calculate the secondary structures of a few residues over time (without manually modifying the ss.xpm file) ?

Thanks for any help!

Regards,

Jianqing


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