[gmx-users] dna-protein complex simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Sep 19 14:03:10 CEST 2008

Hi Prasun,

I converted it using a script of mine (which unfortunately is not in a
shape for shipping yet), and the output file gives me no problem.
Looking at it, I notice a difference (do look at it with a fixed-width

dna.pdb:ATOM   7613  P  DTHY I -72      17.935 138.346  27.497  1.00
out.pdb:ATOM     37  P   DTHYI -72      17.935 138.346  27.497  1.00 81.39

To me it seems I was right that the residue name was shifted. Take
better care when changing residue names.



On 9/19/08, prasun kumar <prasun30 at gmail.com> wrote:
> Hello Tsjerk
> I am attaching a file having a porttion of my PDB file,please check it.Its
> working for all other nucleotides.There is problem only with DTHY
> Thanx in advance
> with regards
> --
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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