Re: Parameter and Topology File Question

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Sun Apr 21 2019 - 07:35:53 CDT

Hello,

Please refer to http://mackerell.umaryland.edu/~kenno/cgenff/program.php#namd

Victor

On Sun, Apr 21, 2019 at 5:45 AM Oscar Bastidas <obastida_at_umn.edu<mailto:obastida_at_umn.edu>> wrote:
Hello,

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:

par_all27_prot_lipid.inp
top_all27_prot_lipid.inp

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

par_all36m_prot.prm
top_all36_prot.rtf

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 Additionally, as I understand it, the tutorial files are somewhat out of date (RMSF profiles from both file sources are vastly different).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

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

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