From: Axel Kohlmeyer (
Date: Wed Mar 17 2010 - 17:20:02 CDT

On Wed, 2010-03-17 at 16:38 -0500, Thomas C. Bishop wrote:

hi tom,

> This brings up a more general question....
> Is it possible to redefine key works in VMD
> and if so how is this done?

some of the "keywords" are actually macros.
check out the output of: atomselect macro

others are hardcoded, so there it gets a bit
more tricky. if there are only a few pieces
missing, perhaps adding them via defining a
new macro (e.g. ambersidechain) might help.

> everything from sidechains etc...
> the reason I ask is that if I load an amber generated
> parmameters/topology
> file VMD can work with it but a number of the predefined key words do
> not
> functional fully correct. e.g.
> "nucleic" misses the default termination of DNA if I"m not mistaken.

is this with vmd-1.8.6 or vmd-1.8.7?


> TOm

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.