[gmx-users] [merge option in pdb2gmx

[David]

On Sun, 2005-05-08 at 16:05 -0400, Valentin Gogonea wrote:
> 
> 
> ______________________________________________________________________
> 
>         Sorry to keep bothering with this but I still don't get it
>         right.
> 
> I deleted two Cys residues from the pdb file , so now I have in the
> PDB file only 2 Cys residues and the ZN ion, each of Cys has a
> different chain letter but the same residue number.  When I use merge
> option , should I answer "y" or should I answer "n" when is asking
> whether to merge the chains? If I answer "y" then one of the Cys is
> deleted and I get an error message:

> deleting duplicate atom    N  CYS2   2  pdb nr  221
> deleting duplicate atom   CA  CYS2   2  pdb nr  222
> deleting duplicate atom   CB  CYS2   2  pdb nr  225
> deleting duplicate atom   SG  CYS2   2  pdb nr  226
> deleting duplicate atom    C  CYS2   2  pdb nr  223
> deleting duplicate atom    O  CYS2   2  pdb nr  224

That still means your pdb file is wrong. If the chain label is in the
wrong column it will not be treated as a chain label.

> Now there are 7 atoms
> No N- or C-terminus found: this chain appears to contain no protein
> Fatal error: Atom -C not found in residue CYS22 while adding hydrogens
> 
> If I answer "n" then the Cys residues and Zn ion are in separate itp
> files with no indication that bonds between Zn and S were made.
> 
> I don't know what I am missing here, but I just can't figure it out.
> 
> Could you please (if you have time) send me the topology files
> correctly created and tell me where the information for bonds between
> Zn and S is stored.
> 
> This may look like a silly example but actually is kind of a model to
> crosslink two monomers of Nitric Oxide Synthase through a Zn-S bridge
> that involves 4 Cys residues coordinated to Zn, two from one monomer
> and the other two from the second monomer.
> 
> Thank you again for the help.
> 
> Valentin
> 
> 
>         Have you tried looking at the coordinates? There' isn't a
>         single peptide 
>         bond here. There are just four cysteines. If you want this to
>         work you'll 
>         have to use four different labels.
>         
>         
>         -- 
>         David.
>         ________________________________________________________________________
>         David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
>         group,
>         Dept. of Cell and Molecular Biology, Uppsala University.
>         Husargatan 3, Box 596,  75124 Uppsala, Sweden
>         phone: 46 18 471 4205 fax: 46 18 511 755
>         spoel at xray.bmc.uu.se spoel at gromacs.org
>         http://xray.bmc.uu.se/~spoel
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>         
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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