VMD-L Mailing List

From: Jason Smith (jason_smith_18_at_sfu.ca)
Date: Fri Jan 15 2021 - 22:17:41 CST

Tiglath,

it'd be a good idea to get a clear understanding of the formats and purpose of the various file types you will be using. PDB, PSF, topology, and parameter files. Having a clearer understanding of file types will also give you a clearer understanding behind how and why NAMD does what it does (at least from the perspective of the force field).

https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html__;!!DZ3fjg!obhUBGy3Rk2Gncn0MVdlE5fmvdsm2Suz4716Syq1rCBgPuwQ_r6iObPsDOP0Bc4UhA$

https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html

https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node25.html

https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html

going through the fftk tutorial and getting a basic understanding of cgenff will also help to re-enforce this, as well as give some clearer insight the list of *.rtf and *.prm and *.str files you might come across for various activities.

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, 15 January 2021 4:37:04 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Question about NAMD configuration files

Hi VMD community

I have a quick question about the parameter files used in NAMD config files. In the NAMD configuration files used in the NAMD tutorial and in the sample.conf, the CHARM parameter file used is: par_all27_prot_lipid.inp. Is there a reason why this particle CHARM file is used? If not, then how can you tell which kind of parameter file should be chosen?

Thanks

Tiglath