VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 08 2007 - 11:29:56 CST

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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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