AMBER: Hydrogen bonding question

From: <>
Date: Tue, 15 Mar 2005 9:57:45 -0500
('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.

At this point I am assuming that the reason for this is that the hydrogen
bonding is not restricted in distance and that leap just picks any
nucleotide that is complimentary to the another nucleotide when making
the prmtop file. This then would lead to unreasonable hydrogen-bonding.
Is there some way that I can restrict the distance nucleotides have to be
from each other to be involved in hydrogen-bonding?
Furthermore, is there some way to do this in the sander input file? I am
asking this, because I am running Amber on a cluster, in which I do not
have any access to the basic amber code. I have it on my workstation, but
when running large scale simulations I do not have access to the sander code.

Best Regards,


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Received on Tue Mar 15 2005 - 15:53:00 PST
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