VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Sep 23 2013 - 07:35:25 CDT

Mohan,

Make sure that the water optimization computation terminated normally, first by checking the Gaussian log file for "Normal termination of Gaussian..." and then by visual inspection using the "Load LOG File" button in ffTK.

To answer your second question, the algorithm for automatic assignment of donor/acceptors is simple: all hydrogens are donors, non-hydrogens with <4 bonded atoms are acceptors, carbons with <4 bonded atoms are both acceptors and donors. This is very much an overly simplistic approach, and meant to serve as a starting point for users to manually modify the selections.

Regards,
Christopher Mayne

On Sep 21, 2013, at 2:23 PM, Mohan maruthi sena wrote:

> Hello Vmd users,
> I trying to find parameters for a organic molecule. After generating initial parameter file , to find out water interaction we find donor acceptors and generate gaussian files. After running gaussian calculation and loading log files , I find some of the water molecules are still lying at the same position as initial gau file. May i know why it happens and what is the criteria to give donor acceptor atoms?
>
>
> Thanks & regards,
> Mohan Maruthi