[gmx-users] Handling protein chain breaks
Mark.Abraham at anu.edu.au
Thu Apr 6 23:26:48 CEST 2006
joao at lnls.br wrote:
> 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.
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