AMBER Archive (2005)

Subject: Re: AMBER: Hydrogen bonding question

From: opitz_at_che.udel.edu
Date: Tue Mar 15 2005 - 09:34:53 CST

('binary' encoding is not supported, stored as-is) >Dear Amber Community,
>
>I am trying to simulate a single strand of an oligonucleotide. This
>results in a the strand folding onto itself in implicit solvent.
>Then I tried to place it in explicit solvent and equilibrate the pressure
>to 1 bar. Then I removed the restraints from the molecule and let it
>move. Agin, this resulted in the strand folding onto itself.
>
>
>
do you have reason to think that this is not correct?

Yes, I am trying to simulate a 12-mer PNA. Other simulations with PNA's,
done by other people in the literature, seem to indicate that PNA's are
not prone to hydrogen-bond onto itself. (Example of this can be seen
here: JACS, 2001, 123, 7414-7422, Srikanta Sen, Lennart Nilsson) So based
on this, I thought that PNA's are not likely to fold onto itself and
hydrogen bond with nucleotides on the other end of the strand. If this is
not the case, is this just an arteract of the program used in the paper
mentioned above? And if this i the case, how can I be more certain of
what to use and what is "more accurate"?
I made the PNA residues and then calculated the charges using antechamber
and the bcc method.

Thanks,

Armin

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