[gmx-users] [merge option in pdb2gmx

Valentin Gogonea v.gogonea at csuohio.edu
Sun May 8 22:05:38 CEST 2005

> 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
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.


> 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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