Re: Problem with running NAMD config file

From: Vermaas, Josh (
Date: Thu Feb 11 2021 - 13:40:57 CST

Ahh! Multiple parameter files all need to be prefixed with "parameters" so the parser doesn't break. Try:

parameters C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36_prot.prm

parameters C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm
#you'll probably also need to add water parameters somewhere?


On 2/11/21 12:28 PM, Tiglath Moradkhan wrote:
Yes. Here it is.

On Wed, Feb 10, 2021 at 8:06 PM "ROPÓN-PALACIOS G." <<>> wrote:
You can attach config file.

Enviado desde mi iPhone

> El 10 feb. 2021, a la(s) 8:04 p. m., Tiglath Moradkhan <<>> escribió:
> To the NAMD community
> I'm a new a NAMD user and I'm trying to equilibrate a lipoprotein system via a simple minimization and equilibration simulation. I've written the required NAMD config file using the NAMD tutorials but when I try running it I get the following error message:
> FATAL ERROR: tried before startup to read config file parameter that was not set
> while executing
> "C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm"
> (file "CSApoA1.conf" line 30)
> I don't understand what the issue is. I've checked online to resolve the issue and found that the .prm extension are for the parameter files so there shouldn't be a problem with providing the correct parameter files. Therefore I'm confused why I'm getting this error message because I got these files from the provided plugin tcl folder.
> I would be very glad for your help.
> Thanks
> Tiglath Moradkhan

Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology<>;!!DZ3fjg!tBZ46npBhXgpE62liIHjaXck1Gcy0oqPJL625oCsHWGf4CoscwdQ5qI3PgBkDSA2WQ$ 

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST