VMD-L Mailing List

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Fri Mar 21 2014 - 06:28:03 CDT

All,
   Thank you for the information. I believe the documentation on ffTK that
you pointed me to is very thorough and should give me a good foundation.
Cheers,
--Jim

On Thu, Mar 20, 2014 at 8:12 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> 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/
>
>
>