From: Brian Bennion (brian_at_youkai.llnl.gov)
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 ?
yes
This question doesn't appear to be a namd issue, instead it is VMD related
and that is another list vmd-l_at_ks.uiuc.edu
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...
Brian
> 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 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 422-6605 ** *****************************************************************
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