[gmx-users] SS bond

[correafe at iq.usp.br]

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 ?

                                    Thanks in advance,
                                                       Fernando