Dear Amber unsers,
I've got another question - I did a MD with weak restraints on a DNA/covalentyl bound drug complex and as soon as I switch to an MD with a MD with constant pressure without SHAKE, the endings of the double strand become unstable. I minimized with caution before. The hydrogen bonds betweens the bases are somewhat present, but the bases aren't orthogonal to the DNA-axis anymore.
I do the simulation with an DNA Decamer. Of coure, I could just elongate the sequence, but upcoming, this complex decamer/drug will be assigned with NMR, and actually, I would like to keep exactly this sequence.
So what to do and what is common? Am i allowed to impose restraints on the endings? Or how you handle such problems.
Thanks a lot in advance.
Michel
"Ein Herz für Kinder" - Ihre Spende hilft! Aktion: www.deutschlandsegelt.de
Unser Dankeschön: Ihr Name auf dem Segel der 1. deutschen America's Cup-Yacht!
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Received on Wed Nov 15 2006 - 06:07:35 PST
