I have MD simulated a homology model in gromacs. I have obtained an RMS fluctuation graph for the same. Can this graph be compared with a PDB file which has b-factors generated during X-ray crystallography of it? As a 5 aa loop in my model is having high fluctuation can I relate this loop with B-factors in a pdb file for the same aligned loop?
Ricardo J Ferreira
Hello.
Ies, it can be compared. But you also can generate beta-factors. In gromacs, do the following: Take the g_rmsf -res output, square it and multiply it by (IIRC) 800 pi^2/3 (you can do all this in xmgrace).
Best regards.
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