Hi all,
Can any one please suggest me a tool or web server or a script for calculating the root mean square fluctuation for side chain, back bones and all atoms. The protein/DNA structures are not from the trajectory. As a part of analysis, I have collected multiple PDB entries of same class of protein. Your helps in this matter is greatly appreciated. Thank you
As you have mentioned you have taken pdb for same class of protein, then why do you want RMSF?
During fluctuation of a dynamical system about some well-defined average position, the RMSD from the average over time can be referred to as the RMSF. Here your protein / DNA are static.
If you want to calculate RMSD, then you can use any software like pymol or vmd etc.
It's to study the structural perturbations in different packing. RMSD is okay, but I need specifically RMSF.
Hi,
using Gromacs software, you can calculate RMSF of many pdb files.
Regards,
Biswajit
But Sir, without doing simulation how can you get rmsf for static structures? I've given the definition for rmsf in my previous answer. Rmsf is something which you calculate for a dynamic system. But here you have taken different pdb structures with different protein.
How did you solve that? I also wanted to understand residue-wise variations of the protein from various crystal structures.
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