[gmx-users] Handling protein chain breaks

[Mark Abraham]

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.

That might work, but I've never tried it on pdb2gmx to see...

> 2. Just comment out the lines in the top file where the atoms involved 
> in this bond appear.

This just wouldn't work - you can't have free valences in conventional 
MM force fields.

> 3. Other options???

Build residues in, per David Mobley's suggestion.