Re: Parameter and Topology File Question

From: Victor Kwan (
Date: Sun Apr 21 2019 - 07:35:53 CDT


Please refer to


On Sun, Apr 21, 2019 at 5:45 AM Oscar Bastidas <<>> wrote:

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 Additionally, as I understand it, the tutorial files are somewhat out of date (RMSF profiles from both file sources are vastly different).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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