Downloading CHARMM Parameter and Topology Files

From: Audrey Salazar (alsalazar_at_northwestern.edu)
Date: Fri Jul 27 2007 - 11:31:54 CDT

Hello,
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://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html#ap-paramfiles),
the following link is given to download the parameter and topology files for
the CHARMM force field:

http://www.pharmacy.umaryland.edu/faculty/amackere/research.html

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:

http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm

***Is http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htmthe
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-paramfilesfor
parameter files with toppar_c31b1/par_all27_prot_lipid.prm and those
from
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node22.htmlwith
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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