I am calculating RMSD using RMSD visualiser tool in VMD. When I calculate before clicking ALIGN button and after aligning through trajectory, I obtain different curves? What reasons causes that?
Hi Onur, as RMSD is an internal descriptor of protein dynamic, the align button align the frames of your trajectory with respect to a reference frame previously to the fit (frame 0 if you dont give any reference). In the case of proteins, another point to take into account is to exclude a few residues of the N and C term of your protein (normally with high mobility) in order to get a better fit.
Well it is simple, as we know there are few kind of movement of molecule, that is rotation, translation, vibration, and bending. The aligning process reduces the effect of rotation and translation of molecule in RMSD analysis which in some case would be more favorable.
Regards,
Radif
Update: It means after the aligning process, the measured RMSD is only the one caused by the change of conformation.
Hi Onur, as RMSD is an internal descriptor of protein dynamic, the align button align the frames of your trajectory with respect to a reference frame previously to the fit (frame 0 if you dont give any reference). In the case of proteins, another point to take into account is to exclude a few residues of the N and C term of your protein (normally with high mobility) in order to get a better fit.
Agree with Diego, as an addition, you might want to use only the backbone atom. I can see that in the picture above the selection is "protein and noh", which is the default I presume, which means the one taken into account is all of the protein atom without hydrogen.
The command for both Diego and I suggested can be found here:
www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node12.html
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