I have run simulation three complexes for 50ns by YASARA. For SSP, YASARA provides a time vs % of Helix, Turn etc. graph but I want to determine a graph of residue vs % of Helix, Turn etc. graph (see attachment for example). I know that GROMACS provides that type of data, but how can I do similar things from YASARA?
Dear Muhammad Shaiful Alam ,
Please find enclosed the pdf that describes details that seems to be close to what you are looking for.
Page 46 provides the set-up and as far as I understand it the secondary structure and hydrogen bonding present in a sequence/protein was analysed using YASARA and custom Python (http://www.python.org) scripts, see for example page 81.
This leads to examples like Figure 4.2 were the time evolution of the secondary structure for each residue during the simulation is shown as well as the percentage of time spent in a secondary structure element by each residue.
Perhaps this comes close to what you are looking for.
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