VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Wed Mar 17 2010 - 16:38:25 CDT

This brings up a more general question....

Is it possible to redefine key works in VMD
and if so how is this done?

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.

TOm

On Wednesday 17 March 2010 01:29:27 pm Balazs Jojart wrote:
> Hello,
> other possibility:
> change allthe Na+ and Cl- in the parameter file to SOD and CLA.
> It doesn't effect the other parameters, and after that, the 'ion' or
> 'ions' keywords are working.
> Cheers,
> Balazs
>
> DimitryASuplatov wrote:
> > Hello,
> >
> > I am running NAMD simulation in AMBER ff and eventually I want to make
> > an index file excluding water and ion molecules in VMD.
> >
> > The problem is that selecting RESNAME NA+ CL- always throws en error.
> > I guess VMD does not like "+" and "-" signs. I`ve tried to mask them
> > with \\, {}, (), "", '' though it did not help.
> >
> > Does anyone know how to make a selection of resname Cl- and Na+ in VMD?
> >
> > Thank you.
>

*******************************
   Thomas C. Bishop
    Tel: 504-862-3370
    Fax: 504-862-8392
http://dna.ccs.tulane.edu
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