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

[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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