From: Tiglath Moradkhan (moradkhantig_at_gmail.com)
Date: Mon Jan 11 2021 - 13:43:00 CST

Hi Jason

OK. Thanks for the help.

Tiglath

On Mon, Jan 11, 2021 at 10:50 AM Jason Smith <jason_smith_18_at_sfu.ca> wrote:

> Where are you pointing to in the config file to tell NAMD to find it?
>
> You can grab it from here:
>
> C:\Program Files (x86)\University of
> Illinois\VMD193\plugins\noarch\tcl\readcharmmpar1.X (1.2, 1.3, 1.5, etc)
>
> then chuck it in the same directory it needs to be in.
>
>
> Personally, I'm lazy, so I have my input files all in the same directory
> that I run the config file from, therefore my config files just look like:
>
>
> # Input
> structure 6lu7-apo_.psf
> coordinates 6lu7-apo_.pdb
>
> paraTypeCharmm on
> parameters par_all36_prot.prm
> parameters par_all36_lipid.prm
> parameters par_all36_na.prm
> parameters par_all36_carb.prm
> parameters par_all36_cgenff.prm
> parameters toppar_all36_carb_glycopeptide.str
> parameters toppar_water_ions_namd.str
> ...
>
>
> Especially useful when keeping up with updated versions of FF, you can
> just go back and open the prm to see what version that sim was run with.
>
> These errors normally come up because of an error in the config file data
> path or because vmd or namd is trying to read/write a file on C:\ in a
> manner windows doesn't like without elevating the exe (in my experience,
> anyway).
>
>
>
>
> Cheers,
> -
> Jason Smith
> Post-Doctoral Fellow
> Robert N. Young Lab, Simon Fraser University
> 8888 University Drive, Burnaby, BC, V5A-1S6
> Canada
>
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Tiglath Moradkhan <moradkhantig_at_gmail.com>
> *Sent:* Friday, 8 January 2021 4:07:43 PM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: Problem with running NAMD configuration file
>
> Hi VMD community
>
> I'm having problems running the NAMD configuration file in the NAMD
> tutorial,
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win.pdf. The
> CHARM file required is par_all27_prot_lipid.inp. However this file does not
> seem to be provided in the tcl plugin folder. The only file is
> par_all27_prot_lipid_na.inp So how can I access the first file? If the
> latter one is the same as the first one, when I try to run the
> configuration file I get the following error message:
>
> "FATAL ERROR: UNABLE TO OPEN CHARMM PARAMETER FILE
> ../common/par_all27_prot_lipid_na.inp"
>
> even though the CHARM file is in the common directory.
>
> I would be very grateful for some help.
>
>
> Thanks
>
> Tiglath
>