[gmx-users] SS bond

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 30 08:11:37 CET 2007

correafe at iq.usp.br wrote:
> Dear gmx users,
> We are trying to make an intermolecular cystine bond between two  
> residues in a dimeric protein (S:S - dist.: 0.203). The initial pdb  
> file should contain the SS bond. Therefore, we used the pdb2gmx -ss  
> -merge to generate the disulfide bond. Apparently it did not form the  
> cystine and added hydrogen atoms (HG). We have increased the cutoff in  
> specbond.dat (directory: /share/top/specbond.dat) from 0.2 to 0.4 and  
> repeated the commands above. We still did not observe the bond  formation.
> Someone could help us ?

They probably need to be in the same PDB chain.


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