VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Mar 28 2013 - 08:03:11 CDT

Updates of geometry (PDB file) and charge (PSF file) are done directly in their respective tabs. The "Update Parameter File with Optimized Parameters" is only used when updating bonds, angles, and dihedrals, after optimization. Note that the "Optimization LOG File" required there is the log file written by ffTK, which contains a portion at the end denoted by "FINAL PARAMETERS" tag, NOT a Gaussian log file.

I strongly suggest viewing the screencasts available on the documentation page: http://www.ks.uiuc.edu/Research/vmd/plugins/fftk

Christopher Mayne

On Mar 28, 2013, at 6:26 AM, Paweł Kędzierski wrote:

> Dear all,
> I have just started playing with FFTK, and want to make sure that I get it correctly.
> As a simple test case I started with H2S molecule and got successfully through most of BuildPar tab; that is, I have assigned LJ parameters and saved optimized geometry as PDB. I checked that the numbers and coords are correct in par and pdb files.
> So far, it means that basic parsing of gausian log file works.
> Now I got to the "Update Parameter File with Optimized Parameters" part.
> When I load the "Optimization LOG File:" and then click the "Write Updated Parameter File" button, the par file is updated (checked by modification time" but the equlibrium parameters (b0 and Theta0) are saved as zeros.
> Is this expected behaviour? Or may it be that the plugin is incompatible with gaussian 2003 (g03) which I use?
> Thank you in advance,
> Pawel
>