Parameter and Topology File Question

From: Oscar Bastidas (
Date: Sun Apr 21 2019 - 04:44:45 CDT


I have noticed that the introductory tutorial parameter and topology files
for starting a NAMD simulation (the protein in the tutorial is ubiquitin)
are named:


whereas the names obtained from CHARMM-GUI/CHARMM are:


The files from the tutorial obviously run when following the tutorial for
setting up and running a simulation on my home computer, but the files from
CHARMM/CHARMM-GUI do not run. Additionally, as I understand it, the
tutorial files are somewhat out of date (RMSF profiles from both file
sources are vastly different).

My question then is, how do I obtain parameter and topology files that are
the most recent *that I can use directly into NAMD and VMD* so that both
NAMD and VMD will take them like the tutorial files? Preferably, I would
like to have NAMD-compatible top and par files that are the equivalent of
charmm36m. Thanks.


Oscar Bastidas, Ph.D.
Postdoctoral Research Associate
University of Minnesota

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