VMD-L Mailing List
From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Sep 03 2015 - 11:20:42 CDT
Make sure that you continue to cc VMD-L so that others can learn from our discussion.
ffTK does not support the NONBONDED (LJ) parameters from first principles; however, the values for these parameters MUST be provided in order to perform several of the optimization calculations. There are two cases:
1) the atom is close enough to a known atom type in the CHARMM/CGenFF parameter set.
--Simply assign the atom type and include the CGenFF parameter files as the "associated parameter file."
2) the atom is not sufficiently close by analogy to any known types and must be assigned a unique atom type.
--Since ffTK does not support the optimization of LJ parameters, you must assign the values of these parameters to the newly created atom type. Typically, you would find the closest match by analogy, and copy the parameters over. The BuildPar -> Assign Missing VDW/LJ Parameters by Analogy tool facilitates this process. The subtlety here is that you are selecting the LJ parameters by analogy, but will not match against any other parameters (bonds, angles, dihedrals) which you want to parameterize explicitly.
On Sep 2, 2015, at 4:55 PM, Chitrak Gupta wrote:
What I meant is this:
The tutorial asks you to assign missing LJ parameters before the Gaussian optimization. My question is, do I HAVE to find a similar atom for each atom in my system? Or is it ok to leave a few of those blank if I can't find one?
Several ffTK features have evolved since the screencasts were made, so some of the precise details between the screencasts and the current version of ffTK have changed; however, the screencasts are still a good guide for beginners.
I'm a little unclear regarding your second question, but I'll take a shot..--_000_5BEE0D7F4EAB400EBF46FFBD267FE1A0illinoisedu_--