VMD-L Mailing List

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Thu Mar 20 2014 - 14:26:40 CDT

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<http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/PARAM_00.pdf>
!
and the link is
http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/PARAM_00.pdf

Sadly, it is also broken...

Cheers,
--Jim