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
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