I don't know what behavior you should have, but ion pairs do have a
tendency to interact in water and are seen in many crystal structures. in
your vacuum simulations I would expect them to be far stronger, and vacuum
simulations should not be used to study behavior in water. Other than that
it is not clear what you are asking.
On Thu, Oct 29, 2015 at 8:05 AM, V. Kumar <vin.vasanth.gmail.com> wrote:
> Dear Amber user
>
> I am trying to calculate structure of an modified peptide using AMBER and
> NMR restraints.
> I have found backbone folding as expected, but I ways seen that the
> side-chains of ASP and GLU -COO(-ve) group is always close to side chain
> -NH3(+ve) of LYS and ARG. I have used 12A° cutoff for non bonded
> interaction. It is commonly observed in vacuum simulated annealing and SPC
> MD.
>
> When I performed the MD in SPC water model with out NMR restraints (only
> from best folded structure) still COO- and HN3+ close effect is not
> removed. Again my initial structure in the end of MD simulation has last
> its folding in the helix part (modified peptide part), where we have more
> hydrogen bonds and I expect that this part should be more rigid.
>
>
> I would highly appreciate if any one share suggestions/idea to tackle this
> problem.
>
> Have a nice day!!!!
>
> thanks
> VK
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Received on Fri Oct 30 2015 - 04:30:03 PDT
