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 Thu Oct 29 2015 - 05:30:03 PDT
