From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 16 2011 - 13:48:43 CDT

Hi,
  You will need to use psfgen (or similar tools) to assemble the
complete model from the individual pieces, as you also have to tie
in the force field parameter files etc too:
  http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 15, 2011 at 08:12:16AM +0200, Christian Wohlschlager wrote:
> Hello !
>
> I maybe fixed the problem of cionize : i did it the following:
>
> I ve a pdp file which doesnt contain the charges of the protein so i
> converted it to .psq with
>
> http://kryptonite.nbcr.net/pdb2pqr/ or another PDB2PQR Web Portal read
>
> :Generation PQR on this page
>
> and then run cionize xxx.pqr (type help at the prompt)
>
> after typing saveion yyy.pdb the i get the pdb file with coordinates of
> the IONS.
>
> Still i dont know how to get a NAMD MD with the two .pdb file ORIGINAL.PDB
> abd IONS.pdb
>
> thank you
>
> christian
>
> Christian Wohlschlager
> JKU Universita:t Linz
> Altenbergerstr.69
> 4040 Linz
> Austria

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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