From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jul 27 2007 - 12:01:34 CDT
1) You have the right link, someone here should update the tutorial.
2) You have the right files as well. The primary differences between
the files provided in the tutorial and the ones you get from
MacKerell's website are the inclusion of CMAP parameters in his
files. NAMD supports these additional parameters now so it's
probably better to use MacKerell's over the ones provided with the
I don't know the logic they use for file extensions but they are
meaningless as far as VMD and NAMD are concerned. Change them to
whatever you like.
On Jul 27, 2007, at 11:31 AM, Audrey Salazar wrote:
> I am a first year graduate student looking to study nucleic acids
> using the all27 force field in NAMD 2.6. The following email will
> contain an explanation of my thinking and questions intermingled
> with it. I will number different parts of my email and I will
> highlight questions with asterisks preceeding them.
> 1) In Appendix 4 of the NAMD 2.6 User's Guide (http://
> node23.html#ap-paramfiles ), the following link is given to
> download the parameter and topology files for the CHARMM force field:
> None of the links on this page, will lead the user to a page from
> which these files can be downloaded. It is my impression that Alex
> Mackerrell's website has been restructured and the correct page is:
> ***Is http://www.pharmacy.umaryland.edu/faculty/amackere/
> force_fields.htm the new URL to the files previously contained on
> http://www.pharmacy.umaryland.edu/faculty/amackere/research.html ?
> If not, would it be possible to direct me to the correct URL?
> 2) I downloaded toppar_c31b1.tar.gz the last web page cited in
> this email. The all27 force field files in toppar_c31b1.tar.gz
> have the following file extensions (.prm for parameter files
> and .rtf (rich text file)). I compared the snippets of code
> available in http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-
> tutorial-unix-html/node23.html#ap-paramfiles for parameter files
> with toppar_c31b1/par_all27_prot_lipid.prm and those from http://
> node22.html with toppar_c31b1/top_all27_prot_lipid.rtf and they
> seem to contain the same information.
> *** Did I download the correct set of parameter and topology files?
> *** Can I safely change the file extensions to .inp for the both
> the topology and parameter files that I downloaded?
> Thank you in advance.
> Audrey Salazar
> Audrey L. Salazar
> Amaral Research Group
> Dept. of Chemical and Biological Engineering Phone: 847.491.2188
> Northwestern University
> Evanston, IL USA
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