Re: uninitialized coordinates

From: Brian Bennion (
Date: Mon Nov 10 2003 - 10:40:31 CST

On Sun, 9 Nov 2003, himanshu chandola wrote:

> hello everyone,
> i am having this problem of having one atom at the
> uninitialized coordinate - way apart from the main atom. Infact even after
> deleting the atom from the vmd delatom i find another atom reappearing
> there. All the atoms that continue reappearing are part of ADP.
> Because of the error appearing for ADP - couldn't find atom C* or
> something like that - i aliased it with C' which was in the param file.
> any comments ?

This question doesn't appear to be a namd issue, instead it is VMD related
and that is another list

also, when using delatom in vmd you have to rewrite the coordinates to a
new file

atomselect0 writepdb temp.pdb

or just delete the offending line from the original pdb file when you
identify it in vmd

But these suggestions are just fixes for a bigger problem, your generation
of the psf file...


> himanshu
> ----------------------------------------
> Morpheus: Do you believe in fate, Neo?
> Neo: No.
> Morpheus: Why Not?
> Neo: Because I don't like the idea that I'm not in control of my life.

**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **

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