VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 20 2014 - 15:22:11 CDT

Jim,
  Thanks for the note. I am CCing people in our team that
are involved with tutorials, and others that have expertise on
this particular topic. We'll try and give you some updates on
this soon.

Cheers,
  John Stone

On Thu, Mar 20, 2014 at 02:26:40PM -0500, Jim Parker wrote:
> Hello,
> I am working through the tutorial on "Parameterizing a Novel Residue",
> and working out the partial charges for my ligand of interest.
>
> In the text, it mentions that "Several concrete examples of this
> charge-fitting strategy are worked
> out in Ref. [7]"
>
> and ref 7 is
> [7] A. Mackerell.
> Parametrization of molecules for use of charmm.
> http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/parameters.html,
> 2003.
>
> But the link is broken. I contacted psc, and they could not find the
> tutorial anymore on their servers.
>
> Does anyone know of an alternate link for the tutorial (or just email
> me...)?
>
> Also, is this the same tutorial mentioned in the ParaTool user guide?
> Section "Outline of parameterization scheme". The link is labeled
> Alex Mackerell's parameter development tutorial!
> and the link is
> http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/PARAM_00.pdf
>
> Sadly, it is also broken...
> Cheers,
> --Jim 

-- 
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/