Jon Ellis wrote:
Hello users
I am using B-factors to look at protein flexibility, using g_rmsf. I
have a 3-ns simulation of an RNA strand bound to a 30-mer peptide. I did
g_rmsf on the complex using the -oq option to obtain the bfac.pdb file,
which gives me the B-factors averaged over the entire trajectory (I think).
Is it reasonable and physically valid to calculate b-factors varying
over time, say by computing g_rmsf for smaller segments of my
trajectory? If so, what would be a reasonable time interval for the
averaging?
In principle yes, but 3 ns is not a lot. You may want to try different
analyses like essential dynamics, and prolong your trajectory.
Thanks in advance for your help
Cheers
Jon
----------------------------------------
Jon Ellis
PhD Candidate, Thompson Group
Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
University of Toronto
Lash Miller 147
(416) 978-6568
[EMAIL PROTECTED]
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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