From: OMAR NABEEL ALY DEMERDASH (ondemerdash_at_wisc.edu)
Date: Mon Jan 08 2007 - 15:17:42 CST

Hi, John and Axel,
Thank you both for prompt responses!! I actually got the gofr function to work. Previously, I think I was using an invalid
selection (too large) for 'max r'. This really is a great tool (thanks to Axel!).
Cheers,
Omar

----- Original Message -----
From: John Stone <johns_at_ks.uiuc.edu>
Date: Monday, January 8, 2007 11:30 am
Subject: Re: vmd-l: error message using gofr
To: OMAR NABEEL ALY DEMERDASH <ondemerdash_at_wisc.edu>
Cc: vmd-l_at_ks.uiuc.edu

> Hi Omar,
> The obvious thinks that you should check are:
> Are your atom selections valid? (neither can be empty)
> Is your frame range valid?
> Both selections must be in the same molecule.
> If you're using PBC, then you cannot have a unit cell with zero volume
> (e.g. a==b==c==0).
> The unit cell must be orthorhomic (at present).
>
> Those are the principle things that could cause you to get an error.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Fri, Jan 05, 2007 at 04:03:12PM -0600, OMAR NABEEL ALY DEMERDASH wrote:
> > Hello,
> > I tried to use the GUI and the tcl command 'measure gofr' for
> measuring g(r) between sodium ions and the protein alpha
> > carbons and got the nonspecific error message: 'measure gofr: error
> during g(r) calculation'. What would be a common cause
> > of a failure to calculate g(r)? I should mention that I am running
> VMD1.8.5 on a Mac OS X version 10.3.9, and the VMD
> > webpage said that VMD1.8.5 is for versions 10.4.5 and later.
> VMD1.8.5 seems to be running OK for basic things like loading
> > molecules. Would the performance of certain newer utilities, such
> as measure gofr, be affected by the version of Mac OS X
> > that vmd is running on?
> > Thanks,
> > Omar Demerdash
>
> --
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> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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