VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Feb 14 2010 - 13:06:20 CST

On Sun, 2010-02-14 at 10:49 -0500, geetha9999_at_aol.com wrote:
> Hi:
>
> I am going through the userguide for psfgenPlugin. It requires the get
> files from the following website to complete the userguide. But the
> following link is not working. Can you please help?

hi!

this is a clear cut case where you can help yourself just as well.

how can somebody use the internet these days and *not* know how
to deal with the fact that URLs are changing? it only requires a
*tiny* amount of common sense.

reason 1) why a URL does not work: the directory structure and
file names have been changed.

strategy: just shorten the url until you find a page that _is_
available and then take it from there. if you just leave out
the "force_fields.htm" part, that would already work in this case.

reason 2) why a URL does not work: the information has been
moved to a different server.

strategy: do a web search with relevant keywords. e.g.:

CHARMM force field parameter topology file

gives the proper URL as the 3rd hit with google (the other two
are tutorials that use CHARMM parameters).

to save you the embarrassment of having to ask how to do a
search with google, here is the result.
http://mackerell.umaryland.edu/CHARMM_ff_params.html

axel.

p.s.: if you post to a mailing list, please don't cc: random
people on top of that. thanks.

>
> 3 BPTI Example
> To actually run this demo requires
> • the program psfgen from any NAMD distribution,
> • the CHARMM topology and parameter files top_all22_prot.inp and
> par_all22_prot.inp from
>
> http://www.pharmacy.umaryland.edu/faculty/amackere/force fields.htm,
>
> Thanks
> Geetha Vasanthakumar
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.