[gmx-users] Handling protein chain breaks

David Mobley dmobley at gmail.com
Thu Apr 6 22:48:42 CEST 2006

You should build in the missing residues. There are various packages
that can do this. Some are Modeller and PLOP. You can probably get
other ideas by searching the mailing list, as this has come up


On 4/6/06, joao at lnls.br <joao at lnls.br> wrote:
> 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.
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