From: Paweł Kędzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Wed Nov 30 2022 - 03:57:16 CST
W dniu 29.11.2022 o 19:02, Rulong Ma pisze:
> Hi the teams of NAMD and VMD.
>
> There is a parameter error in the NAMD Energy of VMD when I calculated
> the interaction energy between protein and RNA.
Dear Rulong,
NAMDEnergy plugin was written for the charmm 27 force field, which was
self-contained, and the GUI only accepts a single parameter file.
Parameters from version 36 are inter-dependent and basically you have to
load all par_all36* parameters files (save for CGenFF) for NAMD to
proceed without such errors, but it is not possible with the current
NAMDEnergy GUI.
The workaround I use is to select the "Debug" checkbox in the GUI, edit
the namd-temp.namd input file to include all needed parameter files, and
run namd manually. But of course this way you loose the plugin
functionality to parse and plot the results. A plotable file of total
energy vs frame number can be easily generated with awk (in Linux):
$ namd2 namd-temp.namd > namd-temp.log
$ awk '/^ENERGY:/{print $2, $12}' namd-temp.log > plot_Etotal.txt
Greetings,
Pawel
>
> The NAMD3 was used to run protein-RNA simulation. However, NAMD
> Energy needs namd2 for energy calculation.
>
> The setting is shown in the following figure. The parameter file is
> "par_all36m_prot.prm". However, after running NAMD energy, there was
> an error. "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN5".
> But I did not find "ATOM HN5" in my simulation system.
>
> when the parameter file is "par_all36_na.prm". There is another
> error, " FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE NH3 ". I
> did not find "ATOM NH3" in my simulation system.
>
> If I did not choose a parameter file, There is another error, " FATAL
> ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1 ". But " ATOM HB1"
> is the atom of Methionine.
>
> Would you help to solve this problem?
>
> image.png
>
>
>
>
>
> --
> Best,
> Rulong Ma
>
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