[gmx-users] [merge option in pdb2gmx
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
> bond here. There are just four cysteines. If you want this to work
> have to use four different labels.
> 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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