VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 11 2021 - 16:22:09 CST

Hi,
  As others mentioned earlier today, your not did not clearly indicate
whether or not you have downloaded the NAMD tutorial files package along
with the PDF. I have double checked the NAMD tutorial files and indeed
the required CHARMM parameter files exist in the tutorial files archive:

% cd namd-tutorial-files/
% ls
1-1-build 1-4-gbis 2-3-energies 2-6-heat-diff 3-2-pullcf
1-2-sphere 2-1-rmsd 2-4-temp 2-7-echoes README
1-3-box 2-2-maxwell 2-5-spec-heat 3-1-pullcv common
% find . -name "*.inp"
./2-7-echoes/common/top_all27_prot_lipid.inp
./2-7-echoes/common/par_all27_prot_lipid.inp
./common/par_all27_prot_lipid.inp
./1-1-build/top_all27_prot_lipid.inp

Please make sure that you have downloaded AND ARE USING the
NAMD tutorial files package, available here (in both .tar.gz and .zip forms):
  http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files.tar.gz
  http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files.zip

You can also view the individual NAMD tutorial files here:
  http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files/

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 08, 2021 at 04:07:43PM -0800, Tiglath Moradkhan wrote:
> 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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/