VMD-L Mailing List
From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Sep 24 2015 - 08:53:36 CDT
> The impropers were generated by fftk
I'm not sure what you mean by this. Impropers are coded in the PSF file, which is created by the user prior to entering the ffTK workflow.
Although it's been on the TODO list for awhile, ffTK doesn't currently support the optimization of improper terms. However, in our experience most small molecules require a shockingly small number of connectivities that require improper terms that are not already defined (check out how short the list of impropers is in CGenFF relative to any of the other terms). Currently, the best way to implement improper terms is to leave them in the PSF, assign the parameters by analogy, and place those parameters into an "associated parameter file" (if you're not already including the CGenFF par file). This will insure that the improper terms are accounted for during the optimizations.
On Sep 24, 2015, at 8:04 AM, Prof. Eddie wrote:
> Hi all,
> I am trying to generate the parameters for a liquid crystal using fftk. As I work though each step I run into a problem. The bond optimization step complains that it does not have the parameters for the two impropers. The impropers were generated by fftk. I can work around this and run the optimization without the impropers, but I feel this will lead to inaccuracies. Is there another way around this?