[gmx-users] Handling protein chain breaks

[joao at lnls.br]

Hi.

I am running dynamics with the protein trypsin. It turns out that it has 
2 aminoacids missing in the middle of the chain. pdb2gmx is making a 
peptide bond between aminoacid i and i+3. Which is the best way to go:

1. Give separate names for the chains before and after the break.
2. Just comment out the lines in the top file where the atoms involved 
in this bond appear.
3. Other options???

Thanks, joao.