From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Mar 20 2014 - 20:12:22 CDT

There’s at least one powerpoint from 2006 linked here: http://mackerell.umaryland.edu/Empirical_FF_Dev.html But even Alex’s webpage has the broken PSC link.

In general though, you should probably look to the latest papers from the MacKerell group. Also our FFTK paper is a pretty good resource; see here http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/ and here http://onlinelibrary.wiley.com/doi/10.1002/jcc.23422/abstract

JC

On Mar 20, 2014, at 3:22 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/