On Fri, May 03, 2013, seçkin Boz wrote:
>
> I'm trying to generate different conformers of small peptides using
> Amber11. These peptides are also protonated at various sites. When proton
> is located at oxygen system blows up.
You likely have zero Lennard-Jones parameters on the proton bound to oxygen.
SHAKE constraints usually prevent such atoms from getting to close to
other negatively charged atoms, but this might not work if they are close in
sequence. Can you say exactly what you mean by "clashed with near N or O
atoms"? What does "near" mean here? Can you give an example?
...dac
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Received on Fri May 03 2013 - 05:30:02 PDT
