VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon May 04 2015 - 11:38:43 CDT

Davide,

Optimized water positions far form the interaction site are indicative of no energy minimum for the specified interaction. Double check that you have properly assigned the water orientation (donor vs acceptor) and inspect the input files to ensure that ffTK has properly positioned the water molecule(s). In some cases, the water interaction profile is strongly perturbed by the local environment, e.g., adjacent atoms. I don't have a lot of experience working with charged species, but I can imagine this will affect the interaction profile.

Regards,
Christopher Mayne

On May 4, 2015, at 8:49 AM, Michetti Davide wrote:

> Hei,
>
> I am following the FFTK tutorial to parametrize an Uracilate anion (negative charge on N1). Looking at the optimization of some donor water, in the water interaction step, I have seen that the one that are interacting with C2, C4, C5 and H5, H6 move really far from the molecule. Is it normal or have I messed up with the setup?
>
> Best,
>
> Davide
>