AMBER Archive (2006)

Subject: AMBER: Restraints of the strand-endings?

From: Michel Becker (
Date: Tue Nov 14 2006 - 14:22:36 CST

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.



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