VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Dec 03 2014 - 15:58:46 CST

Zeinab,

ffTK employs a fairly simplistic algorithm to "autodetect" donors/acceptors. My suggestion is to:

1) use chemical intuition to assess which water orientation is most appropriate
2) you can use the charge data from the geometry optimization Gaussian LOG file to assess #1
3) go ahead and run the water interaction optimization calculations and look at the results to see which ones find reasonable energy minima

Regards,
Christopher Mayne

On Dec 3, 2014, at 7:04 AM, Zeinab Emami wrote:

> Dear VMD experts/ Users,
>
> For water-interaction calculation in ffTK, I am getting extra number of input files for the atoms of my ligands, that is, for some of the carbon atoms, tehre are acceptor input files and donor input files at the same time.
>
> What do you suggest me to do in such cases? To put aside the input files which I think are redundant, or to use all of the corresponding log files for the rest of calculation on ffTK?
>
> Best Regards,
> Zeinab