Dear AMBER community
I am a little confused of the behaviour of my NMR-Refinement and it would be great if you could make any suggestions to my problem.
At first I did a simulated annealing and a small Refinement in implicit solvent. The result was really satisfying ( I am simulating a DNA/drug complex and I know from circular dicroism experiments, that the DNA should look like a B-DNA in the drug/DNA complex as well) and the violation energie was approximatly 6 kcal/molA².
After that I took the output geometries and carried about a NMR-refinement over 1 ns in a TIP3 waterbox. And the result is even better. The DNA looks now like a B-DNA nearly without any pertubations. And the force field shouldn't be overestimated because I set force constants for the NMR-restraints of 50 kcal/molA²and I have employed around 12 restraints per nukleotide. But the violation energy has mor than doubled (~14 kcal/molA²).
I really don't know how to interpret the result. Does I have to take it in account, that the refinement in implicit water ends at 0 K and the MD with NMR-Restraints in explicit water is carried out at 300 K? Or are this violation energies just not comparable? Do you perhaps have literature about because actually we intend to publicate that but right know I do not know what to do.
It would be very nice if you could help me because we are not very experienced in NMR-Refinement. And please excuse my poor English.
With kind regards
Michel
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Received on Sun Feb 18 2007 - 06:07:10 PST
