You likely have zero Lennard-Jones parameters on the proton bound to oxygen.
>
How can I add Lennard-Jones parameter for the proton?
> 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?
>
For example, in the case of asparagine protonated from side chain oxygen;
proton moves close nitrogen in the same side chain. This is the case for
glutamic or aspartic acid acid when one of the oxygens are protonated. I
mean proton moves towards them dragging attached oxygen and touch them.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 03 2013 - 06:00:03 PDT
