VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Tue May 22 2012 - 11:00:41 CDT

Francesco,

As Yi said, the workflow generally follows the tabs moving from left to right.

A good starting point is a thorough reading of the CGenFF paper (http://onlinelibrary.wiley.com/doi/10.1002/jcc.21367/abstract), which details many of the steps ffTK follows. We are also currently working on additional materials that will help users understand the basic functions of ffTK; however, they are not publicly available yet but hopefully will be shortly.

As for what level of QM theory to use for sulphur, that's more of a force field question. There are several threads in the CHARMM user forums, specifically the Parameter Set Discussions, that may help you. See:
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=postlist&Board=12&page=1
Searching for sulphur brings up several relevant posts.

Chris